add_spec_counts: Add spectrum counts

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

Add spectrum counts

Description

DO not aggregate from peptides to proteins. Missing values in peptide tables can inflate protein spectrum counts: median(c(1, NA)) -> 1 not 0.5.

Usage

add_spec_counts(
  dat_dir,
  df_num,
  group_psm_by = "pep_seq_mod",
  group_pep_by = "gene",
  type = "protein"
)

Arguments

dat_dir	A working directory.
df_num	A data frame.
group_psm_by	Group PSM data by.
group_pep_by	Group peptide data by.
type	The type of data.

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