calclfqPepNums: Calculates log2FC of peptides based on LFQ intensity.

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

Calculates log2FC of peptides based on LFQ intensity.

Description

With LFQ, values of log2_R000 (...) and N_log2_R000 (...) in df_num are not yet filled after spreadPepNums. This utility calculates the ratio using the values of LFQ intensity.

Usage

calcLFQPepNums(
  df,
  label_scheme,
  tmt_plex = 0L,
  min_int = 1000,
  imp_refs = FALSE,
  imp_vals = FALSE,
  sp_centers = NULL
)

Arguments

df	A data frame.
label_scheme	Meta data.
tmt_plex	The multiplexicty of TMT.
min_int	Minimal Y intensity to replace 0 values.
imp_refs	Logical; impute missing references or not.
imp_vals	Logical; impute missing values or not.
sp_centers	A vector of log2FC centers for each species.

Details

For SILAC, intensity of heave, light etc. have been spread into multiple columns and thus the log2Ratios can be calculated like regular LFQ.

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