calc_pep_retsd: Calculates the standard deviation in the retention times of...

calc_pep_retsdR Documentation

Calculates the standard deviation in the retention times of peptides.

Description

Different charge states can have small differences in pep_apex_ret, e.g., due to the spikiness of peaks.

Usage

calc_pep_retsd(df, group_psm_by = "pep_seq_mod", use_unique = TRUE)

Arguments

df

A data frame.

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.

use_unique

Logical; if TRUE, filter data by uniqueness.

Details

Sets use_unique = TRUE when used with normPSM where the same group_psm_by can be redundant by prot_acc. Sets use_unique = FALSE when used with mergePep where the same group_psm_by from different samples and LCMS series are all taken into account.


qzhang503/proteoQ documentation built on Dec. 27, 2024, 2:40 p.m.