bgv_lab_prep_count_data_for_deseq2: Preps counts data prior to running gene signature.

In Benjamin-Vincent-Lab/binfotron: Binfotron Bioinformatics Analysis Tools Suite

Preps counts data prior to running gene signature.

Description

bgv_lab_prep_count_data_for_deseq2 is the standard Vincent Lab protocol for preparing gene count data prior to running in DESeq2.

• round_data Rounds data

• require_data_in_samples Requires genes be in 70

• drop_low_columns log2 Drops genes that are in the lowest 10

Usage

bgv_lab_prep_count_data_for_deseq2(my_dt, gene_cols)

Arguments

my_dt	data.table input
gene_cols	Character vector indicating the columns that should be used in the gene signature. Uses operatable_columns. If NULL if will take all numeric columns.

Details

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bgv_lab_prep_count_data_for_deseq2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Benjamin-Vincent-Lab/binfotron documentation built on April 11, 2025, 10:05 p.m.