compareWithNanostring: Comparison with Nanostring

In plger/RNAontheBENCH: RNAontheBENCH - Benchmark of RNAseq quantification and DEA

Description

Loads and processes the RNAseq data before comparing it with the Nanostring quantification. Will produce a number of benchmarking plots and files in the current working directory.

Usage

compareWithNanostring(ANALYSIS_NAME, rnaseq = NULL, qt, normMethod = NULL)

Arguments

ANALYSIS_NAME	A string indicating the name of the analysis/pipeline. Will be used in filenames, plot titles, etc.
rnaseq	The path to the gene-level RNAseq expression matrix. If not given, will look for relevant files in the working directory. The expression matrix should have refseq id or gene symbols in the first column/row.names, and sample names (e.g. 'AJ80') as column headers.
qt	A string indicating the unit of the expression matrix (either "FPKM", "TPM" or "COUNTS").
normMethod	The normalization method to use (see donorm). Defaults to 'housekeeping' for gene-level, and 'TMM' for transcript-level.

Value

Nothing, but produces many files in the working directory...

Examples

# first we create a directory and put the example quantification file in it:
data(exampledata)
dir.create("example")
write.table(exampleGeneLevel,"w12.genes.quant",sep="\t",quote=FALSE)
# then we run the function, giving a name to the analysis, 
# specifying the file and type of quantification:
compareWithNanostring("tophat.featureCount", "w12.genes.quant", qt="COUNTS")

plger/RNAontheBENCH documentation built on May 25, 2019, 8:22 a.m.