normalize_median_of_ratios: normalize_median_of_ratios

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

normalize_median_of_ratios

Description

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

Usage

normalize_median_of_ratios(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 columns of non-normalized counts are replaced in situ with normalized counts. Compare with normalize_median_of_ratios_append.

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

A data frame the same size as the input data frame where non-normalized counts in the 'data.columns' are replaced in situ by normalized counts. Column names are not changed.

Examples

The data set rna_CELP_rpf_count_LMCN contains 17 columns: [1] transcript [2:9] RNA counts [10:17] RPF counts.
RNA and RPF counts are normalized separately.
rna_CELP_rpf_count_norm1_LMCN <- Ribolog::normalize_median_of_ratios(rna_CELP_rpf_count_LMCN, c(2:9))
rna_CELP_rpf_count_norm2_LMCN <- Ribolog::normalize_median_of_ratios(rna_CELP_rpf_count_norm1_LMCN, c(10:17))

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