pad_grp_samples: Pads sample groups.

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

Pads sample groups.

Description

For uses with group searches (with non-trivial values under pep_group). For example, heavy may be missing in complete under one sample and light missing in another.

Usage

pad_grp_samples(
  df,
  sids,
  tmt_levels = NULL,
  type_levels = c("I", "N_I", "sd_log2_R", "log2_R", "N_log2_R")
)

Arguments

df	A data frame.
sids	The Sample_IDs from label_scheme.
tmt_levels	The levels of TMT: 000, 126, 127 etc. without the TMT- prefix.
type_levels	The levels of five types.

Examples

# 10-plex
tmt_levels <- TMT_levels(10)
tmt_levels <- gsub("^TMT-", "", tmt_levels)

group_ids <- c("light", "heavy")

sids <- LETTERS[1:10]
len <- length(sids)
sids <- rep(sids, each = length(group_ids))

group_ids <- rep(group_ids, len)
sids <- paste0(sids, " [", group_ids, "]")

rm(list = c("len", "group_ids"))

# 1-plex
#' tmt_levels <- TMT_levels(1)
tmt_levels <- gsub("^TMT-", "", tmt_levels)

group_ids <- c("light", "heavy")

sids <- LETTERS[1]
len <- length(sids)
sids <- rep(sids, each = length(group_ids))

group_ids <- rep(group_ids, len)
sids <- paste0(sids, " [", group_ids, "]")

rm(list = c("len", "group_ids"))

qzhang503/proteoQ documentation built on Dec. 14, 2024, 12:27 p.m.