psm_mpurge: Helper of purgePSM

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

Helper of purgePSM

Description

Helper of purgePSM

Usage

psm_mpurge(
  file,
  dat_dir = NULL,
  group_psm_by = "pep_seq",
  group_pep_by = "prot_acc",
  pt_cv = NULL,
  max_cv = NULL,
  min_n = 1L,
  rm_allna = FALSE,
  theme,
  ...
)

Arguments

file	A list of file (names).
dat_dir	A character string to the working directory. The default is to match the value under the global environment.
group_psm_by	A character string specifying the method in PSM grouping. At the pep_seq default, descriptive statistics will be calculated based on the same pep_seq groups. At the pep_seq_mod alternative, peptides with different variable modifications will be treated as different species and descriptive statistics will be calculated based on the same pep_seq_mod groups.
group_pep_by	A character string specifying the method in peptide grouping. At the prot_acc default, descriptive statistics will be calculated based on the same prot_acc groups. At the gene alternative, proteins with the same gene name but different accession numbers will be treated as one group.
pt_cv	Numeric between 0 and 1; the percentile of CV. Values above the percentile threshold will be replaced with NA. The default is NULL with no data trimming by CV percentile. The precedence in data purging is pt_cv \ge max_cv \ge min_n.
max_cv	Numeric; the cut-off in maximum CV. Values above the threshold will be replaced with NA. The default is NULL with no data trimming by max CV.
min_n	Positive integer. When calling from purgePSM, peptide entries in PSM tables with the number of identifying PSMs smaller than min_n will be replaced with NA. When calling from purgePep, protein entries in peptide tables with the number of identifying peptides smaller than min_n will be replaced with NA.
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.
theme	A ggplot2 theme, i.e., theme_bw(), or a custom theme. At the NULL default, a system theme will be applied.
...	Additional parameters for plotting: ymax, the maximum y at a log2 scale. ybreaks, the breaks in y-axis at a log2 scale. width, the width of plot. height, the height of plot. flip_coord, logical; if TRUE, flip x and y axis.

qzhang503/proteoQ documentation built on Feb. 27, 2025, 8:34 a.m.