detectionCall

a character string giving the filename of a SAM format file, which is the output of read alignment.

dataset

a character string specifing the species. Options are <code>hg</code> and <code>mm</code>.

species

logical, indicating whether a density plot of detection p values will be generated.

plot

Use GC content adjusted background read counts to determine the detection p values for each gene

Provides powerful and easy-to-use tools for
analyzing next-gen sequencing read data.
Includes quality assessment of sequence reads, read
alignment, read summarization, exon-exon junction detection,
fusion detection, detection of short and long indels, absolute
expression calling and SNP calling. Can be used with reads
generated from any of the major sequencing platforms including
Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and
LifeTech Ion PGM/Proton sequencers.

detectionCall: Determine detection p values for each gene in an RNA-seq dataset

Description

Usage

Arguments

Value