Skip to contents

Export feature EICs for all features

MSdev_export_feature_Chromatographs.Rd

Write {feature_id}.EIC.png for each feature. Prefers stored chromatograms from get_MSdev_Chromatogram (after MSdev_get_feature_chrom); otherwise extracts with get_xcms_feature_chromatogram (not xcms::chromatogram). Set re_extract = TRUE to ignore stored chromatograms and extract with the arguments below. Feature IDs are resolved as in MSdev_export_feature_MSMS. Failures on individual features are warned and skipped.

Usage

MSdev_export_feature_Chromatographs(
  object,
  out.dir = file.path(object@projectInfo$projectDir, "EIC"),
  feature_id = NULL,
  re_extract = FALSE,
  selected_sample = NULL,
  rt = c("expand", "identity", "all"),
  expandRt = 15,
  mz.expand = 0,
  expandMzppm = 2,
  aggregationFun = "max",
  attachPeaks = FALSE,
  BPPARAM = BiocParallel::SerialParam(progressbar = FALSE)
)

Arguments

object

MSdev object

out.dir

Output directory. Default object@projectInfo$projectDir/EIC.

feature_id

Optional character vector of feature IDs. Default all features discovered as above.

re_extract

logical(1). If TRUE, skip stored chromatograms and extract with get_xcms_feature_chromatogram. Default FALSE. Extract arguments (rt, expandRt, mz.expand, expandMzppm, aggregationFun) apply only when extracting; they have no effect on already-stored chromatograms unless re_extract = TRUE.

selected_sample

Sample selection, passed to get_xcms_feature_chromatogram and used to subset stored chromatogram columns. NULL (default) overlays one sample per group (or up to five samples). "maxo" uses the highest-intensity sample; "all" uses all samples; integer indices or sample name(s) select those samples.

rt

one of c("expand", "identity", "all"). Passed to get_xcms_feature_chromatogram when extracting. Default "expand".

expandRt

seconds added each side when rt = "expand". Default 15.

mz.expand

fraction of mz width to expand on each side. Default 0.

expandMzppm

extra m/z pad in ppm applied after mz.expand. Default 2.

aggregationFun

"max" or "sum", passed to get_xcms_feature_chromatogram. Default "max".

attachPeaks

logical; attach feature chromPeaks when extracting. Default FALSE.

BPPARAM

BiocParallel backend for extraction. Default SerialParam(progressbar = FALSE).

Value

Invisible character vector of feature IDs attempted.

See also

MSdev_export_feature_MSMS, get_xcms_feature_chromatogram, get_MSdev_Chromatogram