patchwork.createreference: Patchwork function to create your own normal reference file.

Description Usage Arguments Details Author(s) See Also

View source: R/patchwork.createreference.r

Description

Create your own normal reference file for use with patchwork.plot(). This may have advantages over using the standard issue references. It is recommended to use atleast 3 bamfiles to create a reference file.

Usage

1
patchwork.createreference(...,output="REFOUT")

Arguments

...

The full path and filename to all of the BAM files that you wish to use for creating the reference file. ex patchwork.createreference("file1.bam","file2.bam","file3.bam",etc)

output

Default is "REFOUT". This will result in REFOUT.RData being created in your working directory.

Details

This function will take as its arguments a number of bamfiles that you specify, normalize them according to patchwork.readChroms and patchwork.GCNorm. REFOUT.Rdata, or whichever name you chose, is created in your working directory for further use. This file should then be sent in patchwork.plot to be used as a reference file.

patchwork.plot(bamfile,pileup,reference="path/to/your/REFOUT.Rdata")

Author(s)

Markus Mayrhofer, [email protected] Sebastian DiLorenzo, [email protected]

See Also

patchwork.plot
patchwork.readChroms
patchwork.applyref
patchwork.GCNorm


xu-chang/patchwork-lite documentation built on March 19, 2018, 3:09 a.m.