normCounts: A function to normalize counts

In cshukla/oligoGames: Analyze data from massively parallel reporter assays

Description

This function performs library normalization for the experiment counts

Usage

normCounts(rawCounts = "allTranscriptsCounts_Raw.tsv", normType = "median",
  quantile = 0.5)

Arguments

rawCounts	the name of the file with counts for each oligo. Contains one row per oligo counts with each sample its own column. Please see system.file("inst", "extdata", "allTranscriptsCounts_Raw.tsv", package = "oligoGames") for an example. Make sure that the name of the transcript is in the same format as described in this file. Briefly, it is "GeneName_oligoNum_Barcode". It is critical that oligoNum is second to last and separated by "_". Defaults to allTranscriptsCounts_Raw.tsv.
normType	The method of library normalization the user prefers. Two options: median or quantile. Defaults to median
quantile	The quantile the user wishes to use. Should be a numeric between 0 and 1.

Value

normCounts matrix of normalized counts

Examples

rawCounts = read.table(system.file("extdata", "allTranscriptsCounts_Raw.tsv", package = "oligoGames"), header=T, sep='\t')
normalizedCounts <- normCounts(rawCounts, normType='median')

cshukla/oligoGames documentation built on May 27, 2019, 8:44 a.m.