R/peakPantheR_loadAnnotationParamsCSV.R
In phenomecentre/peakPantheR: Peak Picking and Annotation of High Resolution Experiments
Defines functions
prepare_advanced_target_parameters
check_NA_in_target_parameters
prepare_basic_target_parameters
peakPantheR_loadAnnotationParamsCSV
Documented in
peakPantheR_loadAnnotationParamsCSV
prepare_advanced_target_parameters
prepare_basic_target_parameters
## Init a new peakPantheRAnnotation object after loading ROI, uROI and FIR
## parameters from CSV
#' @title Load fit parameters from CSV
#'
#' @description Initialise a new \code{peakPantheRAnnotation} object after
#' loading ROI, uROI and FIR parameters from CSV. \code{spectraPaths},
#' \code{spectraMetadata} or \code{cpdMetadata} are not initialised and will
#' need to be filled before annotation. \code{useUROI} and \code{useFIR} are set
#' to \code{FALSE} and will need to be set accordingly. \code{uROIExist} is
#' established depending on the uROI columns present in the CSV and will be set
#' to \code{TRUE} only if no \code{NA} are present
#'
#' @param CSVParamPath (str) Path to a CSV file of fit parameters (e.g. as
#' saved by \code{outputAnnotationDiagnostic})
#' @param verbose (bool) If TRUE message progress
#'
#' @return (peakPantheRAnnotation) Object initialised with ROI, uROI and FIR
#' read from the CSV file
#'
#' @export
#'
#' @examples
#' ## Input data
#' input_CSV <- data.frame(matrix(nrow=2,ncol=21,dimnames=list(c(),
#' c('cpdID', 'cpdName',
#' 'X','ROI_rt', 'ROI_mz', 'ROI_rtMin', 'ROI_rtMax','ROI_mzMin','ROI_mzMax',
#' 'X','uROI_rtMin', 'uROI_rtMax', 'uROI_mzMin', 'uROI_mzMax', 'uROI_rt',
#' 'uROI_mz', 'X', 'FIR_rtMin', 'FIR_rtMax', 'FIR_mzMin', 'FIR_mzMax'))))
#' input_CSV[1,] <- c('ID-1', 'Cpd 1', '|', 1., 2., 3., 4., 5., 6., '|',
#' 7., 8., 9., 10., 11., 12., '|', 13., 14., 15., 16.)
#' input_CSV[2,] <- c('ID-2', 'Cpd 2', '|', 17., 18., 19., 20., 21., 22., '|',
#' 23., 24., 25., 26., 27., 28., '|', 29., 30., 31., 32.)
#' input_CSV[,-c(1,2,3,10,17)] <- vapply(input_CSV[,-c(1,2,3,10,17)],
#' as.numeric, FUN.VALUE=numeric(2))
#'
#' # temporary file location
#' savePath1 <- tempfile(pattern='file', tmpdir=tempdir(), fileext='.csv')
#' # save csv
#' utils::write.csv(input_CSV, file=savePath1, row.names=FALSE)
#'
#' # Load parameters from CSV
#' loadedAnnotation <- peakPantheR_loadAnnotationParamsCSV(savePath1,
#' verbose=TRUE)
#' # uROIExist set to TRUE
#' # New peakPantheRAnnotation object initialised for 2 compounds
#' # An object of class peakPantheRAnnotation
#' # 2 compounds in 0 samples.
#' # updated ROI exist (uROI)
#' # does not use updated ROI (uROI)
#' # does not use fallback integration regions (FIR)
#' # is not annotated
peakPantheR_loadAnnotationParamsCSV <- function(CSVParamPath, verbose = TRUE) {
# Check file exist
if (!file.exists(CSVParamPath)) {
stop('specified "CSVParamPath" does not exist')
}
# Read file
tmp_csv <- read.csv(CSVParamPath, header=TRUE, sep=",", quote="\"",
stringsAsFactors=FALSE)
# Process input (either simple or advanced description)
if ("rtMin" %in% colnames(tmp_csv)) {
params <- prepare_basic_target_parameters(tmp_csv)
} else {
params <- prepare_advanced_target_parameters(tmp_csv, verbose=verbose)
}
# Initialise new object
tmp_annotation <- peakPantheRAnnotation(
targetFeatTable=params$targetFeatTable,
uROI=params$uROI,
FIR=params$FIR,
uROIExist=params$uROIExist)
if (verbose) { message('New peakPantheRAnnotation object initialised for ',
nbCompounds(tmp_annotation), ' compounds')
}
return(tmp_annotation)
}
#' Process target region parameters (simple format) for object initialisation
#'
#' Process the simple target region parameters (\code{cpdID, cpdName, mzMin,
#' mzMax, mz, rtMin, rtMax, rt}) and return input variables for
#' \code{peakPantheRAnnotation()}
#'
#' @param paramTable (data.frame) Target region parameters
#'
#' @return (list) List of \code{targetFeatTable, uROI, FIR, uROIExist}
prepare_basic_target_parameters <- function(paramTable){
# Check columns
expected_col <- c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin",
"mz", "mzMax")
if (!(all(expected_col %in% colnames(paramTable)))) {
stop('Columns in "CSVParamPath" must be: "cpdID", "cpdName", "rtMin", ',
'"rt", "rtMax", "mzMin", "mz", "mzMax"')
}
# Prepare ROI, default uROI and FIR
# ensure order
tmp_targetFeatTable <- paramTable[, c("cpdID", "cpdName", "rtMin", "rt",
"rtMax", "mzMin", "mz", "mzMax")]
tmp_targetFeatTable[,c(3:8)] <- vapply(tmp_targetFeatTable[,c(3:8)],
as.numeric, FUN.VALUE=numeric(dim(tmp_targetFeatTable)[1]))
# default values (empty)
tmp_uROI <- data.frame(rtMin=numeric(), rt=numeric(), rtMax=numeric(),
mzMin=numeric(), mz=numeric(), mzMax=numeric(),
stringsAsFactors=FALSE)
tmp_FIR <- data.frame(rtMin=numeric(), rtMax=numeric(), mzMin=numeric(),
mzMax=numeric(), stringsAsFactors=FALSE)
tmp_uROIExist <- FALSE
# check loaded data
# ROI check no NA (stop otherwise crash at next step)
check_NA_in_target_parameters(tmp_targetFeatTable)
# ROI is in order
if ( !(all(tmp_targetFeatTable$rtMin <= tmp_targetFeatTable$rtMax) &
all(tmp_targetFeatTable$mzMin <= tmp_targetFeatTable$mzMax)) ) {
stop('Check ROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')
}
return(list(targetFeatTable=tmp_targetFeatTable, uROI=tmp_uROI, FIR=tmp_FIR,
uROIExist=tmp_uROIExist))
}
# Check if NA in ROI, split function too long
check_NA_in_target_parameters <- function(targetFeatTable) {
if (any(is.na(targetFeatTable[,c("rtMin","rtMax","mzMin","mzMax")]))) {
stop(paste0('Check ROI values: "ROI$rtMin", "ROI$rtMax", ',
'"ROI$mzMin" and "ROI$mzMax" cannot be NA'))
}
}
#' Process target region parameters (with uROI, FIR) for object initialisation
#'
#' Process target region parameters with uROI and FIR (\code{cpdID, cpdName,
#' ROI_rt, ROI_mz, ROI_rtMin, ROI_rtMax, ROI_mzMin, ROI_mzMax, uROI_rtMin,
#' uROI_rtMax, uROI_mzMin, uROI_mzMax, uROI_rt, uROI_mz, FIR_rtMin, FIR_rtMax,
#' FIR_mzMin, FIR_mzMax}) and return input variables for
#' \code{peakPantheRAnnotation()}
#'
#' @param paramTable (data.frame) Target region parameters
#' @param verbose (bool) If TRUE message progress
#'
#' @return (list) List of \code{targetFeatTable, uROI, FIR, uROIExist}
prepare_advanced_target_parameters <- function(paramTable, verbose) {
# Check columns
expected_col <- c("cpdID", "cpdName", "ROI_rt", "ROI_mz", "ROI_rtMin",
"ROI_rtMax", "ROI_mzMin", "ROI_mzMax", "uROI_rtMin",
"uROI_rtMax", "uROI_mzMin", "uROI_mzMax", "uROI_rt",
"uROI_mz", "FIR_rtMin", "FIR_rtMax", "FIR_mzMin",
"FIR_mzMax")
if (!(all(expected_col %in% colnames(paramTable)))) {
stop('Columns in "CSVParamPath" must be: "cpdID", "cpdName", "ROI_rt",',
' "ROI_mz", "ROI_rtMin", "ROI_rtMax", "ROI_mzMin", "ROI_mzMax", ',
'"uROI_rtMin", "uROI_rtMax", "uROI_mzMin", "uROI_mzMax", "uROI_rt"',
', "uROI_mz", "FIR_rtMin", "FIR_rtMax", "FIR_mzMin", "FIR_mzMax"') }
# Prepare ROI, uROI and FIR
tmp_targetFeatTable <- paramTable[,c("cpdID", "cpdName", "ROI_rtMin",
"ROI_rt", "ROI_rtMax", "ROI_mzMin",
"ROI_mz", "ROI_mzMax")]
colnames(tmp_targetFeatTable) <- c("cpdID", "cpdName", "rtMin", "rt",
"rtMax", "mzMin", "mz", "mzMax")
tmp_targetFeatTable[,c(3:8)] <- vapply(tmp_targetFeatTable[,c(3:8)],
as.numeric, FUN.VALUE=numeric(dim(tmp_targetFeatTable)[1]))
tmp_uROI <- paramTable[,c("uROI_rtMin", "uROI_rt", "uROI_rtMax",
"uROI_mzMin", "uROI_mz", "uROI_mzMax")]
colnames(tmp_uROI) <- c("rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax")
tmp_uROI[,c(1,2:6)] <- vapply(tmp_uROI[,c(1,2:6)],
as.numeric, FUN.VALUE=numeric(dim(tmp_targetFeatTable)[1]))
tmp_FIR <- paramTable[,c("FIR_rtMin", "FIR_rtMax", "FIR_mzMin",
"FIR_mzMax")]
colnames(tmp_FIR) <- c("rtMin", "rtMax", "mzMin", "mzMax")
tmp_FIR[,c(1,2:4)] <- vapply(tmp_FIR[,c(1,2:4)],
as.numeric, FUN.VALUE=numeric(dim(tmp_targetFeatTable)[1]))
# establish if uROIExist
tmp_uROIExist <- !any(is.na(tmp_uROI[,c("rtMin", "rtMax", "mzMin",
"mzMax")]))
if (tmp_uROIExist) { if (verbose) { message('uROIExist set to TRUE') }
} else { if (verbose) { message('NA in uROI, uROIExist is set to FALSE') }}
# Check ROI (no NA, is in order)
check_NA_in_target_parameters(tmp_targetFeatTable)
if ( !(all(tmp_targetFeatTable$rtMin <= tmp_targetFeatTable$rtMax) &
all(tmp_targetFeatTable$mzMin <= tmp_targetFeatTable$mzMax)) ) {
stop('Check ROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"') }
# Check uROI is in order (cannot have NA and uROIExist)
if (tmp_uROIExist) {
if ( !(all(tmp_uROI$rtMin <= tmp_uROI$rtMax) &
all(tmp_uROI$mzMin <= tmp_uROI$mzMax)) ) {
stop('Check uROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')}}
return(list(targetFeatTable=tmp_targetFeatTable, uROI=tmp_uROI, FIR=tmp_FIR,
uROIExist=tmp_uROIExist))
}
phenomecentre/peakPantheR documentation built on Feb. 29, 2024, 9:07 p.m.
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Defines functions prepare_advanced_target_parameters check_NA_in_target_parameters prepare_basic_target_parameters peakPantheR_loadAnnotationParamsCSV
Documented in peakPantheR_loadAnnotationParamsCSV prepare_advanced_target_parameters prepare_basic_target_parameters
## Init a new peakPantheRAnnotation object after loading ROI, uROI and FIR
## parameters from CSV
#' @title Load fit parameters from CSV
#'
#' @description Initialise a new \code{peakPantheRAnnotation} object after
#' loading ROI, uROI and FIR parameters from CSV. \code{spectraPaths},
#' \code{spectraMetadata} or \code{cpdMetadata} are not initialised and will
#' need to be filled before annotation. \code{useUROI} and \code{useFIR} are set
#' to \code{FALSE} and will need to be set accordingly. \code{uROIExist} is
#' established depending on the uROI columns present in the CSV and will be set
#' to \code{TRUE} only if no \code{NA} are present
#'
#' @param CSVParamPath (str) Path to a CSV file of fit parameters (e.g. as
#' saved by \code{outputAnnotationDiagnostic})
#' @param verbose (bool) If TRUE message progress
#'
#' @return (peakPantheRAnnotation) Object initialised with ROI, uROI and FIR
#' read from the CSV file
#'
#' @export
#'
#' @examples
#' ## Input data
#' input_CSV <- data.frame(matrix(nrow=2,ncol=21,dimnames=list(c(),
#' c('cpdID', 'cpdName',
#' 'X','ROI_rt', 'ROI_mz', 'ROI_rtMin', 'ROI_rtMax','ROI_mzMin','ROI_mzMax',
#' 'X','uROI_rtMin', 'uROI_rtMax', 'uROI_mzMin', 'uROI_mzMax', 'uROI_rt',
#' 'uROI_mz', 'X', 'FIR_rtMin', 'FIR_rtMax', 'FIR_mzMin', 'FIR_mzMax'))))
#' input_CSV[1,] <- c('ID-1', 'Cpd 1', '|', 1., 2., 3., 4., 5., 6., '|',
#' 7., 8., 9., 10., 11., 12., '|', 13., 14., 15., 16.)
#' input_CSV[2,] <- c('ID-2', 'Cpd 2', '|', 17., 18., 19., 20., 21., 22., '|',
#' 23., 24., 25., 26., 27., 28., '|', 29., 30., 31., 32.)
#' input_CSV[,-c(1,2,3,10,17)] <- vapply(input_CSV[,-c(1,2,3,10,17)],
#' as.numeric, FUN.VALUE=numeric(2))
#'
#' # temporary file location
#' savePath1 <- tempfile(pattern='file', tmpdir=tempdir(), fileext='.csv')
#' # save csv
#' utils::write.csv(input_CSV, file=savePath1, row.names=FALSE)
#'
#' # Load parameters from CSV
#' loadedAnnotation <- peakPantheR_loadAnnotationParamsCSV(savePath1,
#' verbose=TRUE)
#' # uROIExist set to TRUE
#' # New peakPantheRAnnotation object initialised for 2 compounds
#' # An object of class peakPantheRAnnotation
#' # 2 compounds in 0 samples.
#' # updated ROI exist (uROI)
#' # does not use updated ROI (uROI)
#' # does not use fallback integration regions (FIR)
#' # is not annotated
peakPantheR_loadAnnotationParamsCSV <- function(CSVParamPath, verbose = TRUE) {
# Check file exist
if (!file.exists(CSVParamPath)) {
stop('specified "CSVParamPath" does not exist')
}
# Read file
tmp_csv <- read.csv(CSVParamPath, header=TRUE, sep=",", quote="\"",
stringsAsFactors=FALSE)
# Process input (either simple or advanced description)
if ("rtMin" %in% colnames(tmp_csv)) {
params <- prepare_basic_target_parameters(tmp_csv)
} else {
params <- prepare_advanced_target_parameters(tmp_csv, verbose=verbose)
}
# Initialise new object
tmp_annotation <- peakPantheRAnnotation(
targetFeatTable=params$targetFeatTable,
uROI=params$uROI,
FIR=params$FIR,
uROIExist=params$uROIExist)
if (verbose) { message('New peakPantheRAnnotation object initialised for ',
nbCompounds(tmp_annotation), ' compounds')
}
return(tmp_annotation)
}
#' Process target region parameters (simple format) for object initialisation
#'
#' Process the simple target region parameters (\code{cpdID, cpdName, mzMin,
#' mzMax, mz, rtMin, rtMax, rt}) and return input variables for
#' \code{peakPantheRAnnotation()}
#'
#' @param paramTable (data.frame) Target region parameters
#'
#' @return (list) List of \code{targetFeatTable, uROI, FIR, uROIExist}
prepare_basic_target_parameters <- function(paramTable){
# Check columns
expected_col <- c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin",
"mz", "mzMax")
if (!(all(expected_col %in% colnames(paramTable)))) {
stop('Columns in "CSVParamPath" must be: "cpdID", "cpdName", "rtMin", ',
'"rt", "rtMax", "mzMin", "mz", "mzMax"')
}
# Prepare ROI, default uROI and FIR
# ensure order
tmp_targetFeatTable <- paramTable[, c("cpdID", "cpdName", "rtMin", "rt",
"rtMax", "mzMin", "mz", "mzMax")]
tmp_targetFeatTable[,c(3:8)] <- vapply(tmp_targetFeatTable[,c(3:8)],
as.numeric, FUN.VALUE=numeric(dim(tmp_targetFeatTable)[1]))
# default values (empty)
tmp_uROI <- data.frame(rtMin=numeric(), rt=numeric(), rtMax=numeric(),
mzMin=numeric(), mz=numeric(), mzMax=numeric(),
stringsAsFactors=FALSE)
tmp_FIR <- data.frame(rtMin=numeric(), rtMax=numeric(), mzMin=numeric(),
mzMax=numeric(), stringsAsFactors=FALSE)
tmp_uROIExist <- FALSE
# check loaded data
# ROI check no NA (stop otherwise crash at next step)
check_NA_in_target_parameters(tmp_targetFeatTable)
# ROI is in order
if ( !(all(tmp_targetFeatTable$rtMin <= tmp_targetFeatTable$rtMax) &
all(tmp_targetFeatTable$mzMin <= tmp_targetFeatTable$mzMax)) ) {
stop('Check ROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')
}
return(list(targetFeatTable=tmp_targetFeatTable, uROI=tmp_uROI, FIR=tmp_FIR,
uROIExist=tmp_uROIExist))
}
# Check if NA in ROI, split function too long
check_NA_in_target_parameters <- function(targetFeatTable) {
if (any(is.na(targetFeatTable[,c("rtMin","rtMax","mzMin","mzMax")]))) {
stop(paste0('Check ROI values: "ROI$rtMin", "ROI$rtMax", ',
'"ROI$mzMin" and "ROI$mzMax" cannot be NA'))
}
}
#' Process target region parameters (with uROI, FIR) for object initialisation
#'
#' Process target region parameters with uROI and FIR (\code{cpdID, cpdName,
#' ROI_rt, ROI_mz, ROI_rtMin, ROI_rtMax, ROI_mzMin, ROI_mzMax, uROI_rtMin,
#' uROI_rtMax, uROI_mzMin, uROI_mzMax, uROI_rt, uROI_mz, FIR_rtMin, FIR_rtMax,
#' FIR_mzMin, FIR_mzMax}) and return input variables for
#' \code{peakPantheRAnnotation()}
#'
#' @param paramTable (data.frame) Target region parameters
#' @param verbose (bool) If TRUE message progress
#'
#' @return (list) List of \code{targetFeatTable, uROI, FIR, uROIExist}
prepare_advanced_target_parameters <- function(paramTable, verbose) {
# Check columns
expected_col <- c("cpdID", "cpdName", "ROI_rt", "ROI_mz", "ROI_rtMin",
"ROI_rtMax", "ROI_mzMin", "ROI_mzMax", "uROI_rtMin",
"uROI_rtMax", "uROI_mzMin", "uROI_mzMax", "uROI_rt",
"uROI_mz", "FIR_rtMin", "FIR_rtMax", "FIR_mzMin",
"FIR_mzMax")
if (!(all(expected_col %in% colnames(paramTable)))) {
stop('Columns in "CSVParamPath" must be: "cpdID", "cpdName", "ROI_rt",',
' "ROI_mz", "ROI_rtMin", "ROI_rtMax", "ROI_mzMin", "ROI_mzMax", ',
'"uROI_rtMin", "uROI_rtMax", "uROI_mzMin", "uROI_mzMax", "uROI_rt"',
', "uROI_mz", "FIR_rtMin", "FIR_rtMax", "FIR_mzMin", "FIR_mzMax"') }
# Prepare ROI, uROI and FIR
tmp_targetFeatTable <- paramTable[,c("cpdID", "cpdName", "ROI_rtMin",
"ROI_rt", "ROI_rtMax", "ROI_mzMin",
"ROI_mz", "ROI_mzMax")]
colnames(tmp_targetFeatTable) <- c("cpdID", "cpdName", "rtMin", "rt",
"rtMax", "mzMin", "mz", "mzMax")
tmp_targetFeatTable[,c(3:8)] <- vapply(tmp_targetFeatTable[,c(3:8)],
as.numeric, FUN.VALUE=numeric(dim(tmp_targetFeatTable)[1]))
tmp_uROI <- paramTable[,c("uROI_rtMin", "uROI_rt", "uROI_rtMax",
"uROI_mzMin", "uROI_mz", "uROI_mzMax")]
colnames(tmp_uROI) <- c("rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax")
tmp_uROI[,c(1,2:6)] <- vapply(tmp_uROI[,c(1,2:6)],
as.numeric, FUN.VALUE=numeric(dim(tmp_targetFeatTable)[1]))
tmp_FIR <- paramTable[,c("FIR_rtMin", "FIR_rtMax", "FIR_mzMin",
"FIR_mzMax")]
colnames(tmp_FIR) <- c("rtMin", "rtMax", "mzMin", "mzMax")
tmp_FIR[,c(1,2:4)] <- vapply(tmp_FIR[,c(1,2:4)],
as.numeric, FUN.VALUE=numeric(dim(tmp_targetFeatTable)[1]))
# establish if uROIExist
tmp_uROIExist <- !any(is.na(tmp_uROI[,c("rtMin", "rtMax", "mzMin",
"mzMax")]))
if (tmp_uROIExist) { if (verbose) { message('uROIExist set to TRUE') }
} else { if (verbose) { message('NA in uROI, uROIExist is set to FALSE') }}
# Check ROI (no NA, is in order)
check_NA_in_target_parameters(tmp_targetFeatTable)
if ( !(all(tmp_targetFeatTable$rtMin <= tmp_targetFeatTable$rtMax) &
all(tmp_targetFeatTable$mzMin <= tmp_targetFeatTable$mzMax)) ) {
stop('Check ROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"') }
# Check uROI is in order (cannot have NA and uROIExist)
if (tmp_uROIExist) {
if ( !(all(tmp_uROI$rtMin <= tmp_uROI$rtMax) &
all(tmp_uROI$mzMin <= tmp_uROI$mzMax)) ) {
stop('Check uROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')}}
return(list(targetFeatTable=tmp_targetFeatTable, uROI=tmp_uROI, FIR=tmp_FIR,
uROIExist=tmp_uROIExist))
}
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