normalize_median_of_ratios_append: normalize_median_of_ratios_append

In goodarzilab/Ribolog: Logistic-regression-based analysis of ribosome profiling data

normalize_median_of_ratios_append

Description

Function to normalize a RNA-seq or ribo-seq dataset for library size variation

Usage

normalize_median_of_ratios_append(expression.data.frame, data.columns)

Arguments

expression.data.frame	A data frame containing RNA-seq, ribo-seq or similar data. Rows are genes/transcripts and columns are samples. The data frame may contain additional columns for gene/transcript ID or other metadata.
data.columns	A vector of numbers specifying the columns to be normalized together.

Details

The original data columns are retained and normalized columns are added. Compare with normalize_median_of_ratios2.

Use the data.columns argument to exclude gene or transcript ID and other metadata columns from the calculations, and, to normalize RNA and RPF counts separately while keeping them in the same data frame.

Value

An augmented data frame with all the original columns retained and normalized columns appended to the end. New columns are named 'norm.<old_column>'.

Examples

rna_observed_normalized_LMCN <- normalize_median_of_ratios_append(rna_rpf_count_LMCN, c(2:9))

goodarzilab/Ribolog documentation built on Oct. 7, 2022, 10:14 p.m.