R/get_osw_query.R
In Roestlab/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms
Defines functions
getTransitionsQuery
getPeptideQuery2
getPeptideQuery
getPrecursorsQueryID
getFeaturesQuery
getPrecursorsQuery
getAnalytesQuery
getQuery
Documented in
getAnalytesQuery
getFeaturesQuery
getPeptideQuery
getPeptideQuery2
getPrecursorsQuery
getPrecursorsQueryID
getQuery
getTransitionsQuery
#' Generate SQL query to fetch information from osw files.
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2019) + GPL-3
#' Date: 2019-12-14
#' @param maxFdrQuery (numeric) value between 0 and 1. It is used to filter features from osw file which have SCORE_MS2.QVALUE less than itself.
#' @param oswMerged (logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
#' @param analytes (vector of strings) transition_group_ids for which features are to be extracted. analyteInGroupLabel must be set according the pattern used here.
#' @param filename (string) as mentioned in RUN table of osw files.
#' @param runType (char) This must be one of the strings "DIA_Proteomics", "DIA_Metabolomics".
#' @param analyteInGroupLabel (logical) TRUE for getting analytes as PRECURSOR.GROUP_LABEL from osw file.
#' @return SQL query to be searched.
#' @keywords internal
getQuery <- function(maxFdrQuery, oswMerged = TRUE, analytes = NULL,
filename = NULL, runType = "DIA_Proteomics", analyteInGroupLabel = FALSE){
if(is.null(analytes)){
selectAnalytes <- ""
} else{
selectAnalytes <- paste0(" AND transition_group_id IN ('", paste(analytes, collapse="','"),"')")
}
if(oswMerged){
matchFilename <- paste0(" AND RUN.FILENAME ='", filename,"'")
} else{
matchFilename <- ""
}
if(analyteInGroupLabel == TRUE){
transition_group_id <- " PRECURSOR.GROUP_LABEL AS transition_group_id"
} else {
transition_group_id <- " PEPTIDE.MODIFIED_SEQUENCE || '_' || PRECURSOR.CHARGE AS transition_group_id"
}
if(runType == "DIA_Metabolomics"){
query <- paste0("SELECT RUN.ID AS id_run,
COMPOUND.ID AS id_compound,
COMPOUND.COMPOUND_NAME || '_' || COMPOUND.ADDUCTS AS transition_group_id,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id,
RUN.ID AS run_id,
RUN.FILENAME AS filename,
FEATURE.EXP_RT AS RT,
FEATURE.DELTA_RT AS delta_rt,
PRECURSOR.LIBRARY_RT AS assay_RT,
FEATURE.ID AS id,
COMPOUND.SUM_FORMULA AS sum_formula,
COMPOUND.COMPOUND_NAME AS compound_name,
COMPOUND.ADDUCTS AS Adducts,
PRECURSOR.CHARGE AS Charge,
PRECURSOR.PRECURSOR_MZ AS mz,
FEATURE_MS2.AREA_INTENSITY AS Intensity,
FEATURE.LEFT_WIDTH AS leftWidth,
FEATURE.RIGHT_WIDTH AS rightWidth,
SCORE_MS2.RANK AS peak_group_rank,
SCORE_MS2.QVALUE AS m_score
FROM PRECURSOR
INNER JOIN PRECURSOR_COMPOUND_MAPPING ON PRECURSOR.ID = PRECURSOR_COMPOUND_MAPPING.PRECURSOR_ID
INNER JOIN COMPOUND ON PRECURSOR_COMPOUND_MAPPING.COMPOUND_ID = COMPOUND.ID
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
LEFT JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
LEFT JOIN FEATURE_MS1 ON FEATURE_MS1.FEATURE_ID = FEATURE.ID
LEFT JOIN FEATURE_MS2 ON FEATURE_MS2.FEATURE_ID = FEATURE.ID
LEFT JOIN SCORE_MS2 ON SCORE_MS2.FEATURE_ID = FEATURE.ID
WHERE COMPOUND.DECOY = 0 AND SCORE_MS2.QVALUE < ", maxFdrQuery, selectAnalytes, matchFilename, "
ORDER BY transition_group_id,
peak_group_rank;")
} else if (runType == "MRM_Proteomics"){
query <- paste0("SELECT PEPTIDE.MODIFIED_SEQUENCE || '_' || PRECURSOR.CHARGE AS transition_group_id,
RUN.FILENAME AS filename,
FEATURE.EXP_RT AS RT,
FEATURE.DELTA_RT AS delta_rt,
PRECURSOR.LIBRARY_RT AS assay_RT,
FEATURE_MS2.AREA_INTENSITY AS Intensity,
FEATURE.LEFT_WIDTH AS leftWidth,
FEATURE.RIGHT_WIDTH AS rightWidth,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id
FROM PRECURSOR
INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR.ID = PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID AND PRECURSOR.DECOY=0
INNER JOIN PEPTIDE ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
INNER JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
LEFT JOIN FEATURE_MS2 ON FEATURE_MS2.FEATURE_ID = FEATURE.ID
ORDER BY transition_group_id;")
} else{
query <- paste0("SELECT", transition_group_id,",
RUN.FILENAME AS filename,
FEATURE.EXP_RT AS RT,
FEATURE.DELTA_RT AS delta_rt,
PRECURSOR.LIBRARY_RT AS assay_RT,
FEATURE_MS2.AREA_INTENSITY AS Intensity,
FEATURE.LEFT_WIDTH AS leftWidth,
FEATURE.RIGHT_WIDTH AS rightWidth,
SCORE_MS2.RANK AS peak_group_rank,
SCORE_MS2.QVALUE AS m_score,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id
FROM PRECURSOR
INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR.ID = PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID AND PRECURSOR.DECOY=0
INNER JOIN PEPTIDE ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
INNER JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
LEFT JOIN FEATURE_MS2 ON FEATURE_MS2.FEATURE_ID = FEATURE.ID
LEFT JOIN SCORE_MS2 ON SCORE_MS2.FEATURE_ID = FEATURE.ID
WHERE SCORE_MS2.QVALUE < ", maxFdrQuery, selectAnalytes, matchFilename, "
ORDER BY transition_group_id,
peak_group_rank;")
}
return(query)
}
#' Generate SQL query to fetch limited information from osw files.
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2019) + GPL-3
#' Date: 2019-12-14
#' @param maxFdrQuery (numeric) value between 0 and 1. It is used to filter features from osw file which have SCORE_MS2.QVALUE less than itself.
#' @param oswMerged (logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
#' @param filename (string) as mentioned in RUN table of osw files..
#' @param runType (char) This must be one of the strings "DIA_Proteomics", "DIA_Metabolomics".
#' @param analyteInGroupLabel (logical) TRUE for getting analytes as PRECURSOR.GROUP_LABEL from osw file.
#' @return SQL query to be searched.
#' @seealso \code{\link{getOswAnalytes}}
#' @keywords internal
getAnalytesQuery <- function(maxFdrQuery, oswMerged = TRUE, filename = NULL,
runType = "DIA_Proteomics", analyteInGroupLabel = FALSE){
if(oswMerged){
matchFilename <- paste0(" AND RUN.FILENAME ='", filename,"'")
} else{
matchFilename <- ""
}
if(analyteInGroupLabel == TRUE){
transition_group_id <- " PRECURSOR.GROUP_LABEL AS transition_group_id"
} else {
transition_group_id <- " PEPTIDE.MODIFIED_SEQUENCE || '_' || PRECURSOR.CHARGE AS transition_group_id"
}
if(runType == "DIA_Metabolomics"){
query <- paste0("SELECT COMPOUND.ID AS compound_id,
COMPOUND.COMPOUND_NAME || '_' || COMPOUND.ADDUCTS AS transition_group_id,
RUN.FILENAME AS filename,
SCORE_MS2.RANK AS peak_group_rank,
SCORE_MS2.QVALUE AS m_score
FROM PRECURSOR
INNER JOIN PRECURSOR_COMPOUND_MAPPING ON PRECURSOR.ID = PRECURSOR_COMPOUND_MAPPING.PRECURSOR_ID
INNER JOIN COMPOUND ON PRECURSOR_COMPOUND_MAPPING.COMPOUND_ID = COMPOUND.ID
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
LEFT JOIN SCORE_MS2 ON SCORE_MS2.FEATURE_ID = FEATURE.ID
WHERE COMPOUND.DECOY = 0 AND SCORE_MS2.QVALUE < ", maxFdrQuery, matchFilename, "
ORDER BY transition_group_id,
peak_group_rank;")
} else if (runType == "MRM_Proteomics"){
query <- paste0("SELECT PEPTIDE.MODIFIED_SEQUENCE || '_' || PRECURSOR.CHARGE AS transition_group_id,
RUN.FILENAME AS filename,
FEATURE.EXP_RT AS RT,
FROM PRECURSOR
INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR.ID = PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID AND PRECURSOR.DECOY=0
INNER JOIN PEPTIDE ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
ORDER BY transition_group_id;")
} else{
query <- paste0("SELECT", transition_group_id,",
RUN.FILENAME AS filename,
SCORE_MS2.RANK AS peak_group_rank,
SCORE_MS2.QVALUE AS m_score,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id
FROM PRECURSOR
INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR.ID = PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID AND PRECURSOR.DECOY=0
INNER JOIN PEPTIDE ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
INNER JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
LEFT JOIN SCORE_MS2 ON SCORE_MS2.FEATURE_ID = FEATURE.ID
WHERE SCORE_MS2.QVALUE < ", maxFdrQuery, matchFilename, "
ORDER BY transition_group_id,
peak_group_rank;")
}
return(query)
}
# https://stackoverflow.com/questions/10622260/how-do-you-query-an-int-column-for-any-value
#' Get precursor Info
#'
#' For each precursor in the table respective transition ids are fetched.
#' Order of transition is kept same as the order of their intensities in \code{\link{getTransitionsQuery}}.
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2019) + GPL-3
#' Date: 2020-04-04
#' @inheritParams fetchPrecursorsInfo
#' @return SQL query to be searched.
#' @seealso \code{\link{fetchPrecursorsInfo}}
#' @keywords internal
getPrecursorsQuery <- function(runType = "DIA_Proteomics", level = "Peptide")
{
if (runType == "DIA_Proteomics"){
if(level == "Protein"){
query <- "SELECT DISTINCT PRECURSOR.ID AS transition_group_id,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id,
PEPTIDE.ID AS peptide_id,
PEPTIDE.MODIFIED_SEQUENCE AS sequence,
PRECURSOR.CHARGE AS charge,
PRECURSOR.GROUP_LABEL AS group_label
FROM PEPTIDE_PROTEIN_MAPPING
INNER JOIN (
SELECT PROTEIN_ID
FROM SCORE_PROTEIN
WHERE SCORE_PROTEIN.CONTEXT = $CONTEXT AND SCORE_PROTEIN.QVALUE < $FDR
) AS SCORE_PROTEIN ON SCORE_PROTEIN.PROTEIN_ID = PEPTIDE_PROTEIN_MAPPING.PROTEIN_ID
INNER JOIN(
SELECT PEPTIDE_ID
FROM SCORE_PEPTIDE
WHERE SCORE_PEPTIDE.CONTEXT = $CONTEXT AND SCORE_PEPTIDE.QVALUE < $FDR
) AS SCORE_PEPTIDE ON SCORE_PEPTIDE.PEPTIDE_ID = PEPTIDE_PROTEIN_MAPPING.PEPTIDE_ID
INNER JOIN(
SELECT ID, MODIFIED_SEQUENCE
FROM PEPTIDE
WHERE PEPTIDE.DECOY = 0
) AS PEPTIDE ON PEPTIDE_PROTEIN_MAPPING.PEPTIDE_ID = PEPTIDE.ID
LEFT JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID
INNER JOIN (
SELECT ID, CHARGE, GROUP_LABEL
FROM PRECURSOR
WHERE PRECURSOR.DECOY = 0
) AS PRECURSOR ON PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID = PRECURSOR.ID
LEFT JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
ORDER BY peptide_id, transition_group_id, transition_id;"
} else{
query <- "SELECT DISTINCT PRECURSOR.ID AS transition_group_id,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id,
PEPTIDE.ID AS peptide_id,
PEPTIDE.MODIFIED_SEQUENCE AS sequence,
PRECURSOR.CHARGE AS charge,
PRECURSOR.GROUP_LABEL AS group_label
FROM PRECURSOR
INNER JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN PEPTIDE ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID
INNER JOIN (
SELECT PEPTIDE_ID
FROM SCORE_PEPTIDE
WHERE SCORE_PEPTIDE.CONTEXT = $CONTEXT AND SCORE_PEPTIDE.QVALUE < $FDR
) AS SCORE_PEPTIDE ON SCORE_PEPTIDE.PEPTIDE_ID = PEPTIDE.ID
WHERE PRECURSOR.DECOY = 0
ORDER BY peptide_id, transition_group_id, transition_id;"
}
} else if (runType == "DIA_Metabolomics")
{
query <- "SELECT PRECURSOR.ID AS transition_group_id,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id,
PRECURSOR_COMPOUND_MAPPING.COMPOUND_ID AS peptide_id,
COMPOUND.SUM_FORMULA AS sum_formula,
COMPOUND.COMPOUND_NAME AS compound_name,
COMPOUND.ADDUCTS AS adducts,
PRECURSOR.CHARGE AS charge,
PRECURSOR.GROUP_LABEL AS group_label
FROM PRECURSOR
INNER JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN PRECURSOR_COMPOUND_MAPPING ON PRECURSOR_COMPOUND_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN COMPOUND ON PRECURSOR_COMPOUND_MAPPING.COMPOUND_ID = COMPOUND.ID
WHERE PRECURSOR.DECOY = 0
ORDER BY peptide_id, transition_group_id, transition_id;"
}
query
}
#' Get features from a SQLite file
#'
#' Query is generated to identify features below a FDR cut-off from a run.
#'
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2019) + GPL-3
#' Date: 2020-04-07
#' @param runType (char) This must be one of the strings "DIA_Proteomics", "DIA_Metabolomics".
#' @return SQL query to be searched.
#' @seealso \code{\link{fetchFeaturesFromRun}}
#' @keywords internal
getFeaturesQuery <- function(runType = "DIA_Proteomics") #is the same call for both
{
if (runType == "DIA_Proteomics"){
query <- "SELECT PRECURSOR.ID AS transition_group_id,
FEATURE.ID AS feature_id,
FEATURE.EXP_RT AS RT,
FEATURE_MS2.AREA_INTENSITY AS intensity,
FEATURE.LEFT_WIDTH AS leftWidth,
FEATURE.RIGHT_WIDTH AS rightWidth,
SCORE_MS2.RANK AS peak_group_rank,
SCORE_MS2.QVALUE AS m_score
FROM PRECURSOR
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
LEFT JOIN (
SELECT FEATURE_ID, AREA_INTENSITY
FROM FEATURE_MS2
) AS FEATURE_MS2 ON FEATURE_MS2.FEATURE_ID = FEATURE.ID
INNER JOIN (
SELECT FEATURE_ID, RANK, QVALUE
FROM SCORE_MS2
WHERE SCORE_MS2.QVALUE < $FDR
) AS SCORE_MS2 ON SCORE_MS2.FEATURE_ID = FEATURE.ID
WHERE PRECURSOR.DECOY = 0 AND RUN.ID = $runID
ORDER BY transition_group_id, peak_group_rank;"
} else if (runType == "DIA_Metabolomics") {
query <- "SELECT PRECURSOR.ID AS transition_group_id,
FEATURE.ID AS feature_id,
FEATURE.EXP_RT AS RT,
FEATURE_MS2.AREA_INTENSITY AS intensity,
FEATURE.LEFT_WIDTH AS leftWidth,
FEATURE.RIGHT_WIDTH AS rightWidth,
SCORE_MS2.RANK AS peak_group_rank,
SCORE_MS2.QVALUE AS m_score
FROM PRECURSOR
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
LEFT JOIN FEATURE_MS2 ON FEATURE_MS2.FEATURE_ID = FEATURE.ID
LEFT JOIN SCORE_MS2 ON SCORE_MS2.FEATURE_ID = FEATURE.ID
WHERE RUN.ID = $runID AND SCORE_MS2.QVALUE < $FDR AND PRECURSOR.DECOY = 0
ORDER BY transition_group_id, peak_group_rank;"
}
query
}
#' Get precursor Info
#'
#' For each precursor in the table respective transition ids are fetched.
#' Order of transition is kept same as the order of their intensities in \code{\link{getTransitionsQuery}}.
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2020) + GPL-3
#' Date: 2020-04-04
#' @param analytes (integer) A vector of integer that is searched in PRECURSOR.ID.
#' @param runType (char) This must be one of the strings "DIA_Proteomics", "DIA_Metabolomics".
#' @return SQL query to be searched.
#' @seealso \code{\link{fetchPrecursorsInfo}}
#' @keywords internal
getPrecursorsQueryID <- function(analytes, runType = "DIA_Proteomics"){
selectAnalytes <- paste0(" transition_group_id IN ('", paste(analytes, collapse="','"),"')")
if (runType == "DIA_Proteomics"){
query <- paste0("SELECT PRECURSOR.ID AS transition_group_id,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id,
PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID AS peptide_id,
PEPTIDE.MODIFIED_SEQUENCE AS sequence,
PRECURSOR.CHARGE AS charge,
PRECURSOR.GROUP_LABEL AS group_label
FROM PRECURSOR
INNER JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN PEPTIDE ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID
WHERE ", selectAnalytes, "
ORDER BY peptide_id, transition_group_id, transition_id;")
}
else if (runType == "DIA_Metabolomics"){
query <- paste0("SELECT PRECURSOR.ID AS transition_group_id,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id,
PRECURSOR_COMPOUND_MAPPING.COMPOUND_ID AS peptide_id,
COMPOUND.SUM_FORMULA AS sum_formula,
COMPOUND.COMPOUND_NAME AS compound_name,
COMPOUND.ADDUCTS AS adducts,
PRECURSOR.CHARGE AS charge,
PRECURSOR.GROUP_LABEL AS group_label
FROM PRECURSOR
INNER JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN PRECURSOR_COMPOUND_MAPPING ON PRECURSOR_COMPOUND_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN COMPOUND ON PRECURSOR_COMPOUND_MAPPING.COMPOUND_ID = COMPOUND.ID
WHERE ", selectAnalytes, "
ORDER BY peptide_id, transition_group_id, transition_id;")
}
query
}
#' Get peptide scores
#'
#' For each peptide, its score, pvalue and qvalues are fetched across all runs.
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2020) + GPL-3
#' Date: 2020-07-01
#' @param runType (char) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics".
#' @return SQL query to be searched.
#' @seealso \code{\link{getPeptideScores}}
#' @keywords internal
getPeptideQuery <- function(runType = "DIA_Proteomics"){
if(runType == "DIA_Proteomics"){
query <- "SELECT DISTINCT SCORE_PEPTIDE.PEPTIDE_ID AS peptide_id,
SCORE_PEPTIDE.RUN_ID AS run,
SCORE_PEPTIDE.SCORE AS score,
SCORE_PEPTIDE.PVALUE AS pvalue,
SCORE_PEPTIDE.QVALUE AS qvalue
FROM SCORE_PEPTIDE
WHERE SCORE_PEPTIDE.CONTEXT = $CONTEXT;"
} else if(runType == "DIA_Metabolomics"){
query <- "SELECT DISTINCT COMPOUND.ID AS peptide_id,
MIN(SCORE_MS2.QVALUE) AS minV,
FEATURE.RUN_ID AS run,
SCORE_MS2.SCORE AS score,
SCORE_MS2.PVALUE AS pvalue,
SCORE_MS2.QVALUE AS qvalue
FROM SCORE_MS2
INNER JOIN FEATURE ON FEATURE.ID = SCORE_MS2.FEATURE_ID
INNER JOIN PRECURSOR_COMPOUND_MAPPING ON PRECURSOR_COMPOUND_MAPPING.PRECURSOR_ID = FEATURE.PRECURSOR_ID
INNER JOIN COMPOUND ON PRECURSOR_COMPOUND_MAPPING.COMPOUND_ID = COMPOUND.ID
GROUP BY peptide_id, run;"
}
query
}
#' Get peptide scores
#'
#' For each peptide, its score, pvalue and qvalues are fetched across all runs.
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2020) + GPL-3
#' Date: 2020-11-18
#' @param runType (char) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics".
#' @return SQL query to be searched.
#' @seealso \code{\link{getPeptideScores}}
#' @keywords internal
getPeptideQuery2 <- function(runType = "DIA_Proteomics"){
query <- "SELECT DISTINCT SCORE_PEPTIDE.PEPTIDE_ID AS peptide_id,
SCORE_PEPTIDE.RUN_ID AS run,
SCORE_PEPTIDE.SCORE AS score,
SCORE_PEPTIDE.PVALUE AS pvalue,
SCORE_PEPTIDE.QVALUE AS qvalue
FROM SCORE_PEPTIDE
WHERE SCORE_PEPTIDE.CONTEXT = $CONTEXT AND SCORE_PEPTIDE.RUN_ID = $runID;"
query
}
#' Get transitions from a SQLite file
#'
#' Query is generated to identify features and their transitions below a FDR cut-off from a run.
#' Order of transition intensity is kept same as the order of their Ids in \code{\link{getPrecursorsQuery}}.
#'
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2020) + GPL-3
#' Date: 2020-11-15
#' @param runType (char) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics".
#' @return SQL query to be searched.
#' @seealso \code{\link{fetchTransitionsFromRun}, \link{getPrecursorsQueryID}, \link{getPrecursorsQuery}}
#' @keywords internal
getTransitionsQuery <- function(runType = "DIA_Proteomics"){
query <- "SELECT PRECURSOR.ID AS transition_group_id,
FEATURE.ID AS feature_id,
FEATURE.EXP_RT AS RT,
FEATURE_TRANSITION.AREA_INTENSITY AS intensity,
FEATURE.LEFT_WIDTH AS leftWidth,
FEATURE.RIGHT_WIDTH AS rightWidth,
SCORE_MS2.RANK AS peak_group_rank,
SCORE_MS2.QVALUE AS m_score
FROM PRECURSOR
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
LEFT JOIN (
SELECT FEATURE_ID, TRANSITION_ID, AREA_INTENSITY
FROM FEATURE_TRANSITION
) AS FEATURE_TRANSITION ON FEATURE.ID = FEATURE_TRANSITION.FEATURE_ID
INNER JOIN (
SELECT FEATURE_ID, RANK, QVALUE
FROM SCORE_MS2
WHERE SCORE_MS2.QVALUE < $FDR
) AS SCORE_MS2 ON SCORE_MS2.FEATURE_ID = FEATURE.ID
WHERE PRECURSOR.DECOY = 0 AND RUN.ID = $runID
ORDER BY transition_group_id, peak_group_rank, FEATURE_TRANSITION.TRANSITION_ID;"
query
}
Roestlab/DIAlignR documentation built on March 3, 2021, 9:09 a.m.
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Defines functions getTransitionsQuery getPeptideQuery2 getPeptideQuery getPrecursorsQueryID getFeaturesQuery getPrecursorsQuery getAnalytesQuery getQuery
Documented in getAnalytesQuery getFeaturesQuery getPeptideQuery getPeptideQuery2 getPrecursorsQuery getPrecursorsQueryID getQuery getTransitionsQuery
#' Generate SQL query to fetch information from osw files.
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2019) + GPL-3
#' Date: 2019-12-14
#' @param maxFdrQuery (numeric) value between 0 and 1. It is used to filter features from osw file which have SCORE_MS2.QVALUE less than itself.
#' @param oswMerged (logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
#' @param analytes (vector of strings) transition_group_ids for which features are to be extracted. analyteInGroupLabel must be set according the pattern used here.
#' @param filename (string) as mentioned in RUN table of osw files.
#' @param runType (char) This must be one of the strings "DIA_Proteomics", "DIA_Metabolomics".
#' @param analyteInGroupLabel (logical) TRUE for getting analytes as PRECURSOR.GROUP_LABEL from osw file.
#' @return SQL query to be searched.
#' @keywords internal
getQuery <- function(maxFdrQuery, oswMerged = TRUE, analytes = NULL,
filename = NULL, runType = "DIA_Proteomics", analyteInGroupLabel = FALSE){
if(is.null(analytes)){
selectAnalytes <- ""
} else{
selectAnalytes <- paste0(" AND transition_group_id IN ('", paste(analytes, collapse="','"),"')")
}
if(oswMerged){
matchFilename <- paste0(" AND RUN.FILENAME ='", filename,"'")
} else{
matchFilename <- ""
}
if(analyteInGroupLabel == TRUE){
transition_group_id <- " PRECURSOR.GROUP_LABEL AS transition_group_id"
} else {
transition_group_id <- " PEPTIDE.MODIFIED_SEQUENCE || '_' || PRECURSOR.CHARGE AS transition_group_id"
}
if(runType == "DIA_Metabolomics"){
query <- paste0("SELECT RUN.ID AS id_run,
COMPOUND.ID AS id_compound,
COMPOUND.COMPOUND_NAME || '_' || COMPOUND.ADDUCTS AS transition_group_id,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id,
RUN.ID AS run_id,
RUN.FILENAME AS filename,
FEATURE.EXP_RT AS RT,
FEATURE.DELTA_RT AS delta_rt,
PRECURSOR.LIBRARY_RT AS assay_RT,
FEATURE.ID AS id,
COMPOUND.SUM_FORMULA AS sum_formula,
COMPOUND.COMPOUND_NAME AS compound_name,
COMPOUND.ADDUCTS AS Adducts,
PRECURSOR.CHARGE AS Charge,
PRECURSOR.PRECURSOR_MZ AS mz,
FEATURE_MS2.AREA_INTENSITY AS Intensity,
FEATURE.LEFT_WIDTH AS leftWidth,
FEATURE.RIGHT_WIDTH AS rightWidth,
SCORE_MS2.RANK AS peak_group_rank,
SCORE_MS2.QVALUE AS m_score
FROM PRECURSOR
INNER JOIN PRECURSOR_COMPOUND_MAPPING ON PRECURSOR.ID = PRECURSOR_COMPOUND_MAPPING.PRECURSOR_ID
INNER JOIN COMPOUND ON PRECURSOR_COMPOUND_MAPPING.COMPOUND_ID = COMPOUND.ID
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
LEFT JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
LEFT JOIN FEATURE_MS1 ON FEATURE_MS1.FEATURE_ID = FEATURE.ID
LEFT JOIN FEATURE_MS2 ON FEATURE_MS2.FEATURE_ID = FEATURE.ID
LEFT JOIN SCORE_MS2 ON SCORE_MS2.FEATURE_ID = FEATURE.ID
WHERE COMPOUND.DECOY = 0 AND SCORE_MS2.QVALUE < ", maxFdrQuery, selectAnalytes, matchFilename, "
ORDER BY transition_group_id,
peak_group_rank;")
} else if (runType == "MRM_Proteomics"){
query <- paste0("SELECT PEPTIDE.MODIFIED_SEQUENCE || '_' || PRECURSOR.CHARGE AS transition_group_id,
RUN.FILENAME AS filename,
FEATURE.EXP_RT AS RT,
FEATURE.DELTA_RT AS delta_rt,
PRECURSOR.LIBRARY_RT AS assay_RT,
FEATURE_MS2.AREA_INTENSITY AS Intensity,
FEATURE.LEFT_WIDTH AS leftWidth,
FEATURE.RIGHT_WIDTH AS rightWidth,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id
FROM PRECURSOR
INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR.ID = PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID AND PRECURSOR.DECOY=0
INNER JOIN PEPTIDE ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
INNER JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
LEFT JOIN FEATURE_MS2 ON FEATURE_MS2.FEATURE_ID = FEATURE.ID
ORDER BY transition_group_id;")
} else{
query <- paste0("SELECT", transition_group_id,",
RUN.FILENAME AS filename,
FEATURE.EXP_RT AS RT,
FEATURE.DELTA_RT AS delta_rt,
PRECURSOR.LIBRARY_RT AS assay_RT,
FEATURE_MS2.AREA_INTENSITY AS Intensity,
FEATURE.LEFT_WIDTH AS leftWidth,
FEATURE.RIGHT_WIDTH AS rightWidth,
SCORE_MS2.RANK AS peak_group_rank,
SCORE_MS2.QVALUE AS m_score,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id
FROM PRECURSOR
INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR.ID = PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID AND PRECURSOR.DECOY=0
INNER JOIN PEPTIDE ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
INNER JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
LEFT JOIN FEATURE_MS2 ON FEATURE_MS2.FEATURE_ID = FEATURE.ID
LEFT JOIN SCORE_MS2 ON SCORE_MS2.FEATURE_ID = FEATURE.ID
WHERE SCORE_MS2.QVALUE < ", maxFdrQuery, selectAnalytes, matchFilename, "
ORDER BY transition_group_id,
peak_group_rank;")
}
return(query)
}
#' Generate SQL query to fetch limited information from osw files.
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2019) + GPL-3
#' Date: 2019-12-14
#' @param maxFdrQuery (numeric) value between 0 and 1. It is used to filter features from osw file which have SCORE_MS2.QVALUE less than itself.
#' @param oswMerged (logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
#' @param filename (string) as mentioned in RUN table of osw files..
#' @param runType (char) This must be one of the strings "DIA_Proteomics", "DIA_Metabolomics".
#' @param analyteInGroupLabel (logical) TRUE for getting analytes as PRECURSOR.GROUP_LABEL from osw file.
#' @return SQL query to be searched.
#' @seealso \code{\link{getOswAnalytes}}
#' @keywords internal
getAnalytesQuery <- function(maxFdrQuery, oswMerged = TRUE, filename = NULL,
runType = "DIA_Proteomics", analyteInGroupLabel = FALSE){
if(oswMerged){
matchFilename <- paste0(" AND RUN.FILENAME ='", filename,"'")
} else{
matchFilename <- ""
}
if(analyteInGroupLabel == TRUE){
transition_group_id <- " PRECURSOR.GROUP_LABEL AS transition_group_id"
} else {
transition_group_id <- " PEPTIDE.MODIFIED_SEQUENCE || '_' || PRECURSOR.CHARGE AS transition_group_id"
}
if(runType == "DIA_Metabolomics"){
query <- paste0("SELECT COMPOUND.ID AS compound_id,
COMPOUND.COMPOUND_NAME || '_' || COMPOUND.ADDUCTS AS transition_group_id,
RUN.FILENAME AS filename,
SCORE_MS2.RANK AS peak_group_rank,
SCORE_MS2.QVALUE AS m_score
FROM PRECURSOR
INNER JOIN PRECURSOR_COMPOUND_MAPPING ON PRECURSOR.ID = PRECURSOR_COMPOUND_MAPPING.PRECURSOR_ID
INNER JOIN COMPOUND ON PRECURSOR_COMPOUND_MAPPING.COMPOUND_ID = COMPOUND.ID
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
LEFT JOIN SCORE_MS2 ON SCORE_MS2.FEATURE_ID = FEATURE.ID
WHERE COMPOUND.DECOY = 0 AND SCORE_MS2.QVALUE < ", maxFdrQuery, matchFilename, "
ORDER BY transition_group_id,
peak_group_rank;")
} else if (runType == "MRM_Proteomics"){
query <- paste0("SELECT PEPTIDE.MODIFIED_SEQUENCE || '_' || PRECURSOR.CHARGE AS transition_group_id,
RUN.FILENAME AS filename,
FEATURE.EXP_RT AS RT,
FROM PRECURSOR
INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR.ID = PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID AND PRECURSOR.DECOY=0
INNER JOIN PEPTIDE ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
ORDER BY transition_group_id;")
} else{
query <- paste0("SELECT", transition_group_id,",
RUN.FILENAME AS filename,
SCORE_MS2.RANK AS peak_group_rank,
SCORE_MS2.QVALUE AS m_score,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id
FROM PRECURSOR
INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR.ID = PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID AND PRECURSOR.DECOY=0
INNER JOIN PEPTIDE ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
INNER JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
LEFT JOIN SCORE_MS2 ON SCORE_MS2.FEATURE_ID = FEATURE.ID
WHERE SCORE_MS2.QVALUE < ", maxFdrQuery, matchFilename, "
ORDER BY transition_group_id,
peak_group_rank;")
}
return(query)
}
# https://stackoverflow.com/questions/10622260/how-do-you-query-an-int-column-for-any-value
#' Get precursor Info
#'
#' For each precursor in the table respective transition ids are fetched.
#' Order of transition is kept same as the order of their intensities in \code{\link{getTransitionsQuery}}.
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2019) + GPL-3
#' Date: 2020-04-04
#' @inheritParams fetchPrecursorsInfo
#' @return SQL query to be searched.
#' @seealso \code{\link{fetchPrecursorsInfo}}
#' @keywords internal
getPrecursorsQuery <- function(runType = "DIA_Proteomics", level = "Peptide")
{
if (runType == "DIA_Proteomics"){
if(level == "Protein"){
query <- "SELECT DISTINCT PRECURSOR.ID AS transition_group_id,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id,
PEPTIDE.ID AS peptide_id,
PEPTIDE.MODIFIED_SEQUENCE AS sequence,
PRECURSOR.CHARGE AS charge,
PRECURSOR.GROUP_LABEL AS group_label
FROM PEPTIDE_PROTEIN_MAPPING
INNER JOIN (
SELECT PROTEIN_ID
FROM SCORE_PROTEIN
WHERE SCORE_PROTEIN.CONTEXT = $CONTEXT AND SCORE_PROTEIN.QVALUE < $FDR
) AS SCORE_PROTEIN ON SCORE_PROTEIN.PROTEIN_ID = PEPTIDE_PROTEIN_MAPPING.PROTEIN_ID
INNER JOIN(
SELECT PEPTIDE_ID
FROM SCORE_PEPTIDE
WHERE SCORE_PEPTIDE.CONTEXT = $CONTEXT AND SCORE_PEPTIDE.QVALUE < $FDR
) AS SCORE_PEPTIDE ON SCORE_PEPTIDE.PEPTIDE_ID = PEPTIDE_PROTEIN_MAPPING.PEPTIDE_ID
INNER JOIN(
SELECT ID, MODIFIED_SEQUENCE
FROM PEPTIDE
WHERE PEPTIDE.DECOY = 0
) AS PEPTIDE ON PEPTIDE_PROTEIN_MAPPING.PEPTIDE_ID = PEPTIDE.ID
LEFT JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID
INNER JOIN (
SELECT ID, CHARGE, GROUP_LABEL
FROM PRECURSOR
WHERE PRECURSOR.DECOY = 0
) AS PRECURSOR ON PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID = PRECURSOR.ID
LEFT JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
ORDER BY peptide_id, transition_group_id, transition_id;"
} else{
query <- "SELECT DISTINCT PRECURSOR.ID AS transition_group_id,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id,
PEPTIDE.ID AS peptide_id,
PEPTIDE.MODIFIED_SEQUENCE AS sequence,
PRECURSOR.CHARGE AS charge,
PRECURSOR.GROUP_LABEL AS group_label
FROM PRECURSOR
INNER JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN PEPTIDE ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID
INNER JOIN (
SELECT PEPTIDE_ID
FROM SCORE_PEPTIDE
WHERE SCORE_PEPTIDE.CONTEXT = $CONTEXT AND SCORE_PEPTIDE.QVALUE < $FDR
) AS SCORE_PEPTIDE ON SCORE_PEPTIDE.PEPTIDE_ID = PEPTIDE.ID
WHERE PRECURSOR.DECOY = 0
ORDER BY peptide_id, transition_group_id, transition_id;"
}
} else if (runType == "DIA_Metabolomics")
{
query <- "SELECT PRECURSOR.ID AS transition_group_id,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id,
PRECURSOR_COMPOUND_MAPPING.COMPOUND_ID AS peptide_id,
COMPOUND.SUM_FORMULA AS sum_formula,
COMPOUND.COMPOUND_NAME AS compound_name,
COMPOUND.ADDUCTS AS adducts,
PRECURSOR.CHARGE AS charge,
PRECURSOR.GROUP_LABEL AS group_label
FROM PRECURSOR
INNER JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN PRECURSOR_COMPOUND_MAPPING ON PRECURSOR_COMPOUND_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN COMPOUND ON PRECURSOR_COMPOUND_MAPPING.COMPOUND_ID = COMPOUND.ID
WHERE PRECURSOR.DECOY = 0
ORDER BY peptide_id, transition_group_id, transition_id;"
}
query
}
#' Get features from a SQLite file
#'
#' Query is generated to identify features below a FDR cut-off from a run.
#'
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2019) + GPL-3
#' Date: 2020-04-07
#' @param runType (char) This must be one of the strings "DIA_Proteomics", "DIA_Metabolomics".
#' @return SQL query to be searched.
#' @seealso \code{\link{fetchFeaturesFromRun}}
#' @keywords internal
getFeaturesQuery <- function(runType = "DIA_Proteomics") #is the same call for both
{
if (runType == "DIA_Proteomics"){
query <- "SELECT PRECURSOR.ID AS transition_group_id,
FEATURE.ID AS feature_id,
FEATURE.EXP_RT AS RT,
FEATURE_MS2.AREA_INTENSITY AS intensity,
FEATURE.LEFT_WIDTH AS leftWidth,
FEATURE.RIGHT_WIDTH AS rightWidth,
SCORE_MS2.RANK AS peak_group_rank,
SCORE_MS2.QVALUE AS m_score
FROM PRECURSOR
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
LEFT JOIN (
SELECT FEATURE_ID, AREA_INTENSITY
FROM FEATURE_MS2
) AS FEATURE_MS2 ON FEATURE_MS2.FEATURE_ID = FEATURE.ID
INNER JOIN (
SELECT FEATURE_ID, RANK, QVALUE
FROM SCORE_MS2
WHERE SCORE_MS2.QVALUE < $FDR
) AS SCORE_MS2 ON SCORE_MS2.FEATURE_ID = FEATURE.ID
WHERE PRECURSOR.DECOY = 0 AND RUN.ID = $runID
ORDER BY transition_group_id, peak_group_rank;"
} else if (runType == "DIA_Metabolomics") {
query <- "SELECT PRECURSOR.ID AS transition_group_id,
FEATURE.ID AS feature_id,
FEATURE.EXP_RT AS RT,
FEATURE_MS2.AREA_INTENSITY AS intensity,
FEATURE.LEFT_WIDTH AS leftWidth,
FEATURE.RIGHT_WIDTH AS rightWidth,
SCORE_MS2.RANK AS peak_group_rank,
SCORE_MS2.QVALUE AS m_score
FROM PRECURSOR
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
LEFT JOIN FEATURE_MS2 ON FEATURE_MS2.FEATURE_ID = FEATURE.ID
LEFT JOIN SCORE_MS2 ON SCORE_MS2.FEATURE_ID = FEATURE.ID
WHERE RUN.ID = $runID AND SCORE_MS2.QVALUE < $FDR AND PRECURSOR.DECOY = 0
ORDER BY transition_group_id, peak_group_rank;"
}
query
}
#' Get precursor Info
#'
#' For each precursor in the table respective transition ids are fetched.
#' Order of transition is kept same as the order of their intensities in \code{\link{getTransitionsQuery}}.
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2020) + GPL-3
#' Date: 2020-04-04
#' @param analytes (integer) A vector of integer that is searched in PRECURSOR.ID.
#' @param runType (char) This must be one of the strings "DIA_Proteomics", "DIA_Metabolomics".
#' @return SQL query to be searched.
#' @seealso \code{\link{fetchPrecursorsInfo}}
#' @keywords internal
getPrecursorsQueryID <- function(analytes, runType = "DIA_Proteomics"){
selectAnalytes <- paste0(" transition_group_id IN ('", paste(analytes, collapse="','"),"')")
if (runType == "DIA_Proteomics"){
query <- paste0("SELECT PRECURSOR.ID AS transition_group_id,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id,
PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID AS peptide_id,
PEPTIDE.MODIFIED_SEQUENCE AS sequence,
PRECURSOR.CHARGE AS charge,
PRECURSOR.GROUP_LABEL AS group_label
FROM PRECURSOR
INNER JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN PEPTIDE ON PRECURSOR_PEPTIDE_MAPPING.PEPTIDE_ID = PEPTIDE.ID
WHERE ", selectAnalytes, "
ORDER BY peptide_id, transition_group_id, transition_id;")
}
else if (runType == "DIA_Metabolomics"){
query <- paste0("SELECT PRECURSOR.ID AS transition_group_id,
TRANSITION_PRECURSOR_MAPPING.TRANSITION_ID AS transition_id,
PRECURSOR_COMPOUND_MAPPING.COMPOUND_ID AS peptide_id,
COMPOUND.SUM_FORMULA AS sum_formula,
COMPOUND.COMPOUND_NAME AS compound_name,
COMPOUND.ADDUCTS AS adducts,
PRECURSOR.CHARGE AS charge,
PRECURSOR.GROUP_LABEL AS group_label
FROM PRECURSOR
INNER JOIN TRANSITION_PRECURSOR_MAPPING ON TRANSITION_PRECURSOR_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN PRECURSOR_COMPOUND_MAPPING ON PRECURSOR_COMPOUND_MAPPING.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN COMPOUND ON PRECURSOR_COMPOUND_MAPPING.COMPOUND_ID = COMPOUND.ID
WHERE ", selectAnalytes, "
ORDER BY peptide_id, transition_group_id, transition_id;")
}
query
}
#' Get peptide scores
#'
#' For each peptide, its score, pvalue and qvalues are fetched across all runs.
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2020) + GPL-3
#' Date: 2020-07-01
#' @param runType (char) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics".
#' @return SQL query to be searched.
#' @seealso \code{\link{getPeptideScores}}
#' @keywords internal
getPeptideQuery <- function(runType = "DIA_Proteomics"){
if(runType == "DIA_Proteomics"){
query <- "SELECT DISTINCT SCORE_PEPTIDE.PEPTIDE_ID AS peptide_id,
SCORE_PEPTIDE.RUN_ID AS run,
SCORE_PEPTIDE.SCORE AS score,
SCORE_PEPTIDE.PVALUE AS pvalue,
SCORE_PEPTIDE.QVALUE AS qvalue
FROM SCORE_PEPTIDE
WHERE SCORE_PEPTIDE.CONTEXT = $CONTEXT;"
} else if(runType == "DIA_Metabolomics"){
query <- "SELECT DISTINCT COMPOUND.ID AS peptide_id,
MIN(SCORE_MS2.QVALUE) AS minV,
FEATURE.RUN_ID AS run,
SCORE_MS2.SCORE AS score,
SCORE_MS2.PVALUE AS pvalue,
SCORE_MS2.QVALUE AS qvalue
FROM SCORE_MS2
INNER JOIN FEATURE ON FEATURE.ID = SCORE_MS2.FEATURE_ID
INNER JOIN PRECURSOR_COMPOUND_MAPPING ON PRECURSOR_COMPOUND_MAPPING.PRECURSOR_ID = FEATURE.PRECURSOR_ID
INNER JOIN COMPOUND ON PRECURSOR_COMPOUND_MAPPING.COMPOUND_ID = COMPOUND.ID
GROUP BY peptide_id, run;"
}
query
}
#' Get peptide scores
#'
#' For each peptide, its score, pvalue and qvalues are fetched across all runs.
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2020) + GPL-3
#' Date: 2020-11-18
#' @param runType (char) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics".
#' @return SQL query to be searched.
#' @seealso \code{\link{getPeptideScores}}
#' @keywords internal
getPeptideQuery2 <- function(runType = "DIA_Proteomics"){
query <- "SELECT DISTINCT SCORE_PEPTIDE.PEPTIDE_ID AS peptide_id,
SCORE_PEPTIDE.RUN_ID AS run,
SCORE_PEPTIDE.SCORE AS score,
SCORE_PEPTIDE.PVALUE AS pvalue,
SCORE_PEPTIDE.QVALUE AS qvalue
FROM SCORE_PEPTIDE
WHERE SCORE_PEPTIDE.CONTEXT = $CONTEXT AND SCORE_PEPTIDE.RUN_ID = $runID;"
query
}
#' Get transitions from a SQLite file
#'
#' Query is generated to identify features and their transitions below a FDR cut-off from a run.
#' Order of transition intensity is kept same as the order of their Ids in \code{\link{getPrecursorsQuery}}.
#'
#' @author Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca}
#'
#' ORCID: 0000-0003-3500-8152
#'
#' License: (c) Author (2020) + GPL-3
#' Date: 2020-11-15
#' @param runType (char) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics".
#' @return SQL query to be searched.
#' @seealso \code{\link{fetchTransitionsFromRun}, \link{getPrecursorsQueryID}, \link{getPrecursorsQuery}}
#' @keywords internal
getTransitionsQuery <- function(runType = "DIA_Proteomics"){
query <- "SELECT PRECURSOR.ID AS transition_group_id,
FEATURE.ID AS feature_id,
FEATURE.EXP_RT AS RT,
FEATURE_TRANSITION.AREA_INTENSITY AS intensity,
FEATURE.LEFT_WIDTH AS leftWidth,
FEATURE.RIGHT_WIDTH AS rightWidth,
SCORE_MS2.RANK AS peak_group_rank,
SCORE_MS2.QVALUE AS m_score
FROM PRECURSOR
INNER JOIN FEATURE ON FEATURE.PRECURSOR_ID = PRECURSOR.ID
INNER JOIN RUN ON RUN.ID = FEATURE.RUN_ID
LEFT JOIN (
SELECT FEATURE_ID, TRANSITION_ID, AREA_INTENSITY
FROM FEATURE_TRANSITION
) AS FEATURE_TRANSITION ON FEATURE.ID = FEATURE_TRANSITION.FEATURE_ID
INNER JOIN (
SELECT FEATURE_ID, RANK, QVALUE
FROM SCORE_MS2
WHERE SCORE_MS2.QVALUE < $FDR
) AS SCORE_MS2 ON SCORE_MS2.FEATURE_ID = FEATURE.ID
WHERE PRECURSOR.DECOY = 0 AND RUN.ID = $runID
ORDER BY transition_group_id, peak_group_rank, FEATURE_TRANSITION.TRANSITION_ID;"
query
}
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