calcLFQprnnums: Adds the 'total', 'razor' and 'unique' intensities of...

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

Adds the total, razor and unique intensities of proteins.

Description

Adds the total, razor and unique intensities of proteins.

Usage

calcLFQprnnums(
  df,
  label_scheme,
  use_unique_pep = TRUE,
  group_psm_by = "pep_seq",
  group_pep_by = "gene",
  method_pep_prn = "lfq_top_3_sum",
  impute_prot_na = TRUE,
  use_spec_counts = FALSE
)

Arguments

df	A data frame.
label_scheme	Meta data.
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.
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.
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.
impute_prot_na	Logical; impute NA values of protein log2FC or not.
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.