In PriceLab/rnaSeqNormalization: rnaSeqNormalizer: Cory Funk's favorite methods

options(width=120)
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Overview

RNA-seq data comes from many sources in many forms. The goal of this package is to collect a full bag of tricks and techniques to transform that variety into our (that is, Cory Funk's) preferred standard form.

Load the libraries we need

library(rnaSeqNormalizer)
library(RUnit)

Read in a small tsv file included in this package

file <- system.file(package="rnaSeqNormalizer", "extdata", "tbl.ensg.column.16x10.tsv")
tbl.small <- read.table(file, sep="\t", as.is=TRUE)
checkEquals(dim(tbl.small), c(16, 10))
head(tbl.small)
````

Use the "asinh" algorithm and use maximum median value to select among duplicated gene symbols
sometimes produced in the mapping from ENSG ids.

```r
normalizer <- rnaSeqNormalizer(tbl.small, algorithm="asinh", duplicate.selection.statistic="median")
mtx.asinh.median <- getNormalizedMatrix(normalizer)
fivenum(mtx.asinh.median)
head(mtx.asinh.median)
hist(as.numeric(mtx.asinh.median))

Session Info

```r sessionInfo() ````

PriceLab/rnaSeqNormalization documentation built on Jan. 23, 2020, 4:48 a.m.