calcPeptide: Calculates peptide data for individual TMT experiments

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

Calculates peptide data for individual TMT experiments

Description

Argument injn_idx does not currently used.

Usage

calcPeptide(
  df = NULL,
  group_psm_by = "pep_seq",
  method_psm_pep = "median",
  group_pep_by = "prot_acc",
  dat_dir = NULL,
  set_idx = 1L,
  injn_idx = 1L,
  TMT_plex = 10L,
  lfq_ret_tol = 60L,
  rm_allna = FALSE,
  type_sd = "log2_R"
)

Arguments

df	A data frame containing the PSM table from database searches.
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.
method_psm_pep	Character string; the method to summarize the log2FC and the intensity of PSMs by peptide 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_2_sum for LFQ. The log10-intensity of reporter (or LFQ) ions at the PSMs levels will be the weight when summarizing log2FC with various "top_n" statistics or "weighted_mean".
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.
dat_dir	A character string to the working directory. The default is to match the value under the global environment.
set_idx	Numeric. The index of a multiplex TMT experiment in metadata files such as label_scheme.xlsx and frac_scheme.xlsx.
injn_idx	Numeric. The index of LCMS_Inj in metadata files such as label_scheme.xlsx and frac_scheme.xlsx.
TMT_plex	Numeric; the multiplexity of TMT, i.e., 10, 11 etc.
lfq_ret_tol	The tolerance of retention time (in seconds) for the aggregation of LFQ data.
rm_allna	Logical; if TRUE, removes data rows that are exclusively NA across ratio columns of log2_R126 etc. The setting also applies to log2_R000 in LFQ.
type_sd	Character string; the type of log2Ratios for SD calculations. The value is one log2_R, N_log2_R or Z_log2_R.

qzhang503/proteoQ documentation built on March 16, 2024, 5:27 a.m.