procPSMs: Processes PSMs.

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

Processes PSMs.

Description

Common routines in PSM processing across search engines.

Usage

procPSMs(
  dat_dir = NULL,
  df = NULL,
  scale_rptr_int = FALSE,
  rptr_intco = 0,
  rptr_intrange = c(0, 100),
  rm_craps = FALSE,
  rm_krts = FALSE,
  rm_allna = FALSE,
  annot_kinases = FALSE,
  plot_rptr_int = TRUE,
  parallel = TRUE
)

Arguments

dat_dir	A character string to the working directory. The default is to match the value under the global environment.
df	PSM data.
scale_rptr_int	Logical; if TRUE, scales (up) MS2 reporter-ion intensities by MS1 precursor intensity: I_{MS1}*(I_{x}/\sum I_{MS2}). I_{MS1}, MS1 precursor intensity; I_{MS2}, MS2 reporter-ion intensity; I_{x}, MS2 reporter-ion intensity under TMT channel x. Note that the scaling will not affect log2FC.
rptr_intco	Numeric; the threshold of reporter-ion intensity (TMT: I126 etc.; LFQ: I000) being considered non-trivial. The default is 0 without cut-offs. The data nullification will not be applied synchronously to the precursor intensity (pep_tot_int) under the same PSM query. To guard against odds such as higher MS2 reporter-ion intensities than their contributing MS1 precursor intensity, employs for example filter_... = rlang::exprs(pep_tot_int >= my_ms1_cutoff) during PSM2Pep. The rule of thumb is that pep_tot_int is a single column; thus the corresponding data filtration against it may be readily achieved without introducing new arguments. By contrast, rptr_intco applies to a set of columns, I126 etc.; it might be slightly more involved/laborious when applying suitable statements of filter_ varargs.
rptr_intrange	Numeric vector at length two. The argument specifies the range of reporter-ion intensities (TMT: I126 etc.; LFQ: I000) being considered non-trivial. The default is between 0 and 100 percentile without cut-offs. While argument rptr_intco employs a universal cut-off across samples by absolute values, range_int provides an alternative means of sample-specific thresholding of intensities by percentiles. The data nullification will not be applied synchronously to the precursor intensity under the same PSM query.
rm_craps	Logical; if TRUE, cRAP proteins will be removed. The default is FALSE.
rm_krts	Logical; if TRUE, keratin entries will be removed. The default is FALSE.
rm_allna	Logical; if TRUE, removes data rows that are exclusively NA across ratio columns of log2_R126 etc. The setting also applies to log2_R000 in LFQ.
annot_kinases	Logical; if TRUE, proteins of human or mouse origins will be annotated with their kinase attributes. The default is FALSE.
plot_rptr_int	Logical; if TRUE, the distributions of reporter-ion intensities will be plotted. The default is TRUE. The argument is also applicable to the precursor intensity with MaxQuant LFQ.

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