rm_fully_empty_tmt_sets: Removes fully empty TMT sets.

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

Removes fully empty TMT sets.

Description

If all Sample_ID's are Empty within a TMT_Set. The whole set of experiment, namely all TMT_Channel's, will be removed. Otherwise, Empty sample IDs will still be kept (in that the number of Sample_IDs within a TMT_Set will be always equal to the multiplexity of a TMT experiment).

Usage

rm_fully_empty_tmt_sets(
  df,
  frac_smry = NULL,
  TMT_plex = 0L,
  dat_dir = NULL,
  ext = NULL
)

Arguments

df	A data frame of metadata (e.g., label_scheme_full).
frac_smry	A character string to a .xlsx file containing peptide fractionation summary. The default is frac_smry.xlsx.
TMT_plex	The multiplexity of TMT.
dat_dir	A character string to the working directory. The default is to match the value under the global environment.
ext	The extension of a file name.

Details

The utility is also applicable to LFQ with a special handling at TMT_plex = 0 (not 1).

Sample IDs started with Empty are at first replaced with NA.

qzhang503/proteoQ documentation built on April 13, 2025, 8:31 a.m.