bgv_lab_prep_count_data_for_gene_signature: 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_gene_signature is the standard Vincent Lab protocol for preparing gene count data prior to running gene signatures.

• require_data_in_samples reuires the gene be expressed in 70

• normalize_rows_by_quartile upper quartile normalizes the data

• log_transform_plus log2 transforms (counts + 1)

Usage

bgv_lab_prep_count_data_for_gene_signature(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_gene_signature ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

See Also

Other gene_signature: calculate_gene_signatures()

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