spreadPepNums: Spreads peptide numbers.

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

Spreads peptide numbers.

Description

Spreads fields of numeric values: sd_log2_R, log2_R, log2_R, I, N_I by TMT sets.

Usage

spreadPepNums(
  df,
  basenames,
  group_psm_by,
  ok_mbr = FALSE,
  use_spec_counts = FALSE
)

Arguments

df	A data frame of peptide table.
basenames	Names of peptide table files.
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.
ok_mbr	Logical Capable of MBR or not.
use_spec_counts	Logical; If TRUE, uses spectrum counts for quantitation with Mascot or Mzion outputs.

Details

Also works for LFQ as each sample corresponds to a TMT set.

For single SILAC sample, the values of log2Ratios spreads into MULTIPLE columns of heavy, light etc. Despite, log2Ratios remains NA, just like regular single-sample LFQ. The log2Ratios will be later calculated with calcLFQPepNums that are based on intensity values.

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