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Group features by EIC similarity within RT tolerance

MSdev_group_feature_EIC.Rd

Per-polarity wrapper around xcms_group_feature_EIC. Reuses chromatograms from MSdev_get_feature_chrom, updates MS1 feature_group labels, and optionally stores per-sample sparse similarity matrices in otherData(xcms)$EIC_Similarity.

Usage

MSdev_group_feature_EIC(
  object,
  rt_tol = 5,
  threshold = 0.5,
  expandRt = 2,
  min_width = 20,
  selected_sample = NULL,
  forceExtractChrom = FALSE,
  keep_Similarity_Matrix = TRUE,
  absent_sim = 0,
  method = c("complete_linkage", "hclust_average"),
  n_chunks = NULL,
  BPPARAM = SnowParam(workers = parallel::detectCores() - 1, progressbar = TRUE)
)

Arguments

object

MSdev object

rt_tol

numeric(1). Maximum absolute RT difference (seconds) for which EIC similarity is computed. Default 5.

threshold

numeric(1). Similarity cut-off for the chosen method (see xcms_group_feature_EIC). Default 0.5.

expandRt

numeric(1). Seconds added on each side of each feature's peakRtMin/peakRtMax window when cropping EICs via XChromatograms_subset_feature before correlation. Default 2.

min_width

numeric(1). Minimum RT window width (seconds) after expandRt; shorter windows are padded equally on both sides. Default 20.

selected_sample

NULL, integer index/indices, or sample name(s) (sample.name / chromatogram colnames). NULL uses all samples.

forceExtractChrom

logical(1). If TRUE, (re)extract chromatograms via MSdev_get_feature_chrom even if already stored.

keep_Similarity_Matrix

logical(1). Passed to xcms_group_feature_EIC. Default TRUE.

absent_sim

numeric(1). Passed to xcms_group_feature_EIC. Default 0; set NA for unknown absents.

method

character(1). Grouping method passed to xcms_group_feature_EIC: "complete_linkage" or "hclust_average". Default "complete_linkage".

n_chunks

NULL or positive integer. Passed to xcms_group_feature_EIC / get_xcms_feature_EIC_similarity. Use on large batch projects to avoid oversized Snow payloads (e.g. 200L).

BPPARAM

BiocParallel backend for chromatogram extraction and EIC similarity scoring.

Value

MSdev object with updated MS1 feature_group labels; when keep_Similarity_Matrix is TRUE, also otherData(xcms)$EIC_Similarity on each polarity's MS1 object.