@@ -1,7 +1,7 @@

 1.2

     - added calculatePowerDetectSomatic

     - added getSexFromVcf

-    - added calculateBamCoverageFromInterval

+    - added calculateBamCoverageByInterval

 1.0

     - added correctCoverageBias

@@ -10,6 +10,7 @@ export(correctCoverageBias)

 export(findFocal)

 export(readCurationFile)

 export(calculatePowerDetectSomatic)

+export(calculateBamCoverageByInterval)

 export(createCurationFile)

 export(createNormalDatabase)

 export(createSNPBlacklist)

similarity index 95%

rename from R/calculateBamCoverageFromInterval.R

rename to R/calculateBamCoverageByInterval.R

@@ -1,4 +1,4 @@

-calculateBamCoverageFromInterval <- structure(

+calculateBamCoverageByInterval <- structure(

 function(# Function to calculate coverage from BAM file

 ### Takes a BAM file and an interval file as input and 

 ### returns coverage for each interval.

@@ -52,5 +52,5 @@ output.file=NULL

 }, ex=function() {

 gc.gene.file <- system.file("extdata", "example_gc.gene.file.txt", 

     package="PureCN")

-# calculateBamCoverageFromInterval(bam.file, gc.gene.file)   

+# calculateBamCoverageByInterval(bam.file, gc.gene.file)   

 })    

similarity index 74%

rename from man/calculateBamCoverageFromInterval.Rd

rename to man/calculateBamCoverageByInterval.Rd

@@ -1,9 +1,9 @@

-\name{calculateBamCoverageFromInterval}

-\alias{calculateBamCoverageFromInterval}

+\name{calculateBamCoverageByInterval}

+\alias{calculateBamCoverageByInterval}

 \title{Function to calculate coverage from BAM file}

 \description{Takes a BAM file and an interval file as input and 

 returns coverage for each interval.}

-\usage{calculateBamCoverageFromInterval(bam.file, interval.file, 

+\usage{calculateBamCoverageByInterval(bam.file, interval.file, 

     output.file = NULL)}

 \arguments{

   \item{bam.file}{Filename of a BAM file.}

@@ -23,5 +23,5 @@ readCoverageGatk function.}

 \examples{

 gc.gene.file <- system.file("extdata", "example_gc.gene.file.txt", 

     package="PureCN")

-# calculateBamCoverageFromInterval(bam.file, gc.gene.file)   

+# calculateBamCoverageByInterval(bam.file, gc.gene.file)   

 }

@@ -82,7 +82,7 @@ provided in \software{GATK DepthOfCoverage} format:

 \Biocpkg{PureCN} will only use data from the columns "Target",

 "total\_coverage", and "average\_coverage", all other columns are optional. If

 \software{GATK} is not available, then the

-\Rfunction{calculateBamCoverageFromInterval} function can be used to generate

+\Rfunction{calculateBamCoverageByInterval} function can be used to generate

 the required coverage data from BAM files.  We also refer to the

 \CRANpkg{ExomeCNV} \cite{Sathirapongsasuti2011} package and documentation,

 which provides different scripts for generating coverage files from BAM files.