calc_tmt_prnnums: Helper: calculates the TMT log2FC and reporter-ion intensity...

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

Helper: calculates the TMT log2FC and reporter-ion intensity of proteins

Description

Helper: calculates the TMT log2FC and reporter-ion intensity of proteins

Usage

calc_tmt_prnnums(
  df,
  use_unique_pep = TRUE,
  id = "prot_acc",
  method_pep_prn = "median",
  use_spec_counts = FALSE
)

Arguments

df	A data frame.
use_unique_pep	Logical. If TRUE, only entries that are TRUE or equal to 1 under the column pep_isunique in Peptide.txt will be used, for summarizing the log2FC and the intensity of peptides into protein values. The default is to use unique peptides only. For MaxQuant data, the levels of uniqueness are according to the pep_unique_by in normPSM. The argument currently do nothing to Spectrum Mill data where both unique and shared peptides will be kept.
id	Always "prot_acc".
method_pep_prn	Character string; the method to summarize the the intensity of peptides by protein entries. The descriptive statistics includes c("mean", "median", "weighted_mean", "top_3_mean", "lfq_max", "lfq_top_2_sum", "lfq_top_3_sum", "lfq_all") with median being the default for TMT and lfq_top_3_sum for LFQ. The representative log10-intensity of reporter (or LFQ) ions at the peptide levels will be the weight when summarizing log2FC with various "top_n" statistics or "weighted_mean". The method to summarize log2FC is median.
use_spec_counts	Logical; If TRUE, uses spectrum counts for quantitation with Mascot or Mzion outputs.

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