cleanupPSM: Cleans Up PSM results

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

Cleans Up PSM results

Description

cleanupPSM removes PSM outliers after splitPSM_ma or , splitPSM_mq. The outlier removals will be assessed at the basis of per peptide per TMT channel.

Usage

cleanupPSM(
  dat_dir = NULL,
  rm_outliers = FALSE,
  group_psm_by = "pep_seq",
  rm_allna = FALSE,
  parallel = TRUE
)

Arguments

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.
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.
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.

Details

Dixon's method will be used when 2 < n \le 25; Rosner's method will be used when n > 25.

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