my_complete_cases: Complete cases among sample IDs in label_scheme_sub, not...

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

Complete cases among sample IDs in label_scheme_sub, not label_scheme

Description

Complete cases among sample IDs in label_scheme_sub, not label_scheme

Usage

my_complete_cases(df, scale_log2r, label_scheme_sub)

Arguments

df	The name of a primary data file. By default, it will be determined automatically after matching the types of data and analysis with an id among c("pep_seq", "pep_seq_mod", "prot_acc", "gene"). A primary file contains normalized peptide or protein data and is among c("Peptide.txt", "Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt"). For analyses require the fields of significance p-values, the df will be one of c("Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt").
scale_log2r	Logical; if TRUE, adjusts log2FC to the same scale of standard deviation across all samples. The default is TRUE. At scale_log2r = NA, the raw log2FC without normalization will be used.
label_scheme_sub	A data frame. Subset entries from label_scheme for selected samples.

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