CNVcallFromDB: CNVcallFromDB This function execute the CNV call based on...

In elmerfer/CNVR: This package is a wrapper to ExomeDepth package in order to facilitate the processign of Exome data for oncogenomics and presicion medicine

CNVcallFromDB This function execute the CNV call based on ExomeDepth. The subjects should be already in the Exon DB count database LoadDB

Description

CNVcallFromDB This function execute the CNV call based on ExomeDepth. The subjects should be already in the Exon DB count database LoadDB

Usage

CNVcallFromDB(db, dbSubjects, reference = c("auto","all"))
It assumes that the Subject is not present on the current Exon Count DB.
If the subjects is already in the DB, it will stop.

Arguments

db	exon counts database
dbSubjects	the subjects to test
reference	the reference type

Details

The subjects should be already in the DB by calling AddNewReference. Then the test subject should be identified by it colnames(db$DB). if moretha one subject is referred, then all the subjects in the DB, except the one tested, will be used to build the reference according to the "reference" type used. if reference == auto , then the reference will be chosen by correlation if reference == all , all the remainders subjects will be summed up to build the reference

Examples

## Not run: 
DB <- LoadDB("path/to/db/RDS")
DB <- AddNewReference(db=DB, 
sbjsBamFiles = "/..../PATIENTS/27040/27040_1.fastq.gz.subread.BAM",save=TRUE)
CNVs <- CNVcallFromDB(DB, "27040")

## End(Not run)

elmerfer/CNVR documentation built on July 8, 2022, 6:23 p.m.