RCAS pre-release v0.99.2

Made two minor revisions asked by the reviewer:

• manual loading of some packages manually in the vignette is cancelled
• a NOTE flagged by R CMD Check about a global variable has been fixed

RCAS pre-release v0.99.1

RCAS 0.99.1

This is the version of RCAS R package that has passed the automatic tests on Bioconductor on all available platforms.

installation

library('devtools')
devtools::install_github('BIMSBbioinfo/RCAS')

usage:

First download input datasets from ENSEMBL (GTF file) and doRiNA (BED file) (or use built-in 'testdata' instead)

GTF file:

wget ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz
gunzip Homo_sapiens.GRCh37.75.gtf.gz

Generate an annotation report using the GTF file and built-in test data (BED format) as input.

library('RCAS')
#RCAS::runReport(gffFilePath = "Homo_sapiens.GRCh37.75.gtf",  queryFilePath = "testdata", msigdbFilePath = "testdata", genomeVersion = 'hg19')