pep_to_prn: Helper of Pep2Prn

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

Helper of Pep2Prn

Description

Helper of Pep2Prn

Usage

pep_to_prn(
  id = "prot_acc",
  method_pep_prn = "median",
  use_unique_pep = TRUE,
  gn_rollup = TRUE,
  rm_outliers = FALSE,
  rm_allna = FALSE,
  is_prot_lfq = FALSE,
  engine = "mz",
  impute_prot_na = TRUE,
  use_mq_prot = FALSE,
  use_mf_prot = FALSE,
  use_spec_counts = FALSE,
  ...
)

Arguments

id	Character string; one of pep_seq, pep_seq_mod, prot_acc and gene.
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_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.
gn_rollup	Logical; if TRUE, rolls up protein accessions to gene names.
rm_outliers	Logical; if TRUE, PSM outlier removals will be performed for peptides with more than two identifying PSMs. Dixon's method will be used when 2 < n \le 25 and Rosner's method will be used when n > 25. The default is FALSE.
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.
engine	The name of search engine.
impute_prot_na	Logical; impute NA values of protein log2FC or not.
use_mq_prot	Logical; use MQ protein table or not.
use_mf_prot	Logical; use MSFragger protein table or not.
use_spec_counts	Logical; If TRUE, uses spectrum counts for quantitation with Mascot or Mzion outputs.
...	filter_: Variable argument statements for the filtration of data rows. Each statement contains a list of logical expression(s). The lhs needs to start with filter_. The logical condition(s) at the rhs needs to be enclosed in exprs with round parenthesis. For example, pep_len is a column key in Peptide.txt. The statement of filter_peps_at = exprs(pep_len <= 50) will remove peptide entries with pep_len > 50.

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