R/data.R

In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

#' Extracted-ion chromatograms (XICs) of a peptide
#'
#' @description
#'  XICs of peptide QFNNTDIVLLEDFQK/3 from three SWATH runs:
#'
#' run0 : hroest_K120808_Strep10\%PlasmaBiolRepl1_R03_SW_filt.chrom.mzML\cr
#' run1 : hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML\cr
#' run2 : hroest_K120809_Strep10\%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML
#'
#' @format A list of three elements where each element consists of a list of six data frames. Each
#'  data frame has two columns:
#' \describe{
#'   \item{time}{Retention time of ananlyte in the run, in sec}
#'   \item{intensity}{Intensity of signal for the transition}
#' }
#' @source Raw files are downloaded from \href{http://www.peptideatlas.org/PASS/PASS01508}{Peptide Atlas}.
#' File test_GenerateData.R has \href{https://github.com/shubham1637/DIAlignR/tree/master/data-raw}{source code}
#' to generate the example data.
"XIC_QFNNTDIVLLEDFQK_3_DIAlignR"

#' Analytes information from osw files
#'
#' @description
#'  analytes info from three SWATH runs:
#'
#' run0 : hroest_K120808_Strep10\%PlasmaBiolRepl1_R03_SW_filt.chrom.mzML\cr
#' run1 : hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML\cr
#' run2 : hroest_K120809_Strep10\%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML
#'
#' @format A list of three elements where each element consists of a dataframe:
#' \describe{
#'   \item{transition_group_id}{ID of each peptide}
#'   \item{RT}{Retention time, in sec}
#'   \item{intensity}{Inensity of associated feature}
#'   \item{leftWidth}{Left width of the peak, in sec}
#'   \item{rightWidth}{Right width of the peak, in sec}
#'   \item{peak_group_rank}{Ranking of associated feature}
#'   \item{m_score}{qvalue of associated feature}
#' }
#' @source Raw files are downloaded from \href{http://www.peptideatlas.org/PASS/PASS01508}{Peptide Atlas}.
#' File test_GenerateData.R has \href{https://github.com/shubham1637/DIAlignR/tree/master/data-raw}{source code}
#' to generate the example data.
"oswFiles_DIAlignR"


#' Analytes information from multipeptide.
#'
#' @description
#'  analytes info from three SWATH runs:
#'
#' run0 : hroest_K120808_Strep10\%PlasmaBiolRepl1_R03_SW_filt.chrom.mzML\cr
#' run1 : hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML\cr
#' run2 : hroest_K120809_Strep10\%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML
#'
#' @format A list of 199 elements where each element represents a precursor and consists of a dataframe:
#' \describe{
#'   \item{transition_group_id}{ID of each precursor. Same as the name of the list}
#'   \item{RT}{Retention time, in sec}
#'   \item{intensity}{Inensity of associated feature}
#'   \item{leftWidth}{Left width of the peak, in sec}
#'   \item{rightWidth}{Right width of the peak, in sec}
#'   \item{peak_group_rank}{Ranking of associated feature}
#'   \item{m_score}{qvalue of associated feature}
#'   \item{run}{Name of the run, feature is from}
#'   \item{alignment_rank}{Rank of the feature after alignment}
#' }
#' @source Raw files are downloaded from \href{http://www.peptideatlas.org/PASS/PASS01508}{Peptide Atlas}.
#' File test_GenerateData.R has \href{https://github.com/shubham1637/DIAlignR/tree/master/data-raw}{source code}
#' to generate the example data.
"multipeptide_DIAlignR"