PSCBS (version 0.23.0)

report.PairedPSCBS: Generates a report of the Paired PSCBS results

Description

Generates a report of the Paired PSCBS results.

Usage

## S3 method for class 'PairedPSCBS':
report(fit, sampleName=getSampleName(fit), studyName, ..., rootPath="reports/", verbose=FALSE)

Arguments

fit

A PairedPSCBS object as returned by segmentByPairedPSCBS().

sampleName

A character string specifying the name of the tumor-normal pair segmented.

studyName

A character string specifying the name of study/project.

...

Optional arguments passed to the RSP template.

rootPath

The root directory where to write the report.

verbose

See Verbose.

Value

• Returns the pathname of the generated PDF.

See Also

For more information see PairedPSCBS.

Examples

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Load SNP microarray data
# (note to package developers: this example data set may
#  be replaced in a future release of the package)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
pathname <- system.file("data-ex/PairedPSCBS,exData,chr01.Rbin", package="PSCBS")
data <- R.utils::loadObject(pathname)
str(data)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Paired PSCBS segmentation
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Drop single-locus outliers
dataS <- dropSegmentationOutliers(data)

# Speed up example by segmenting fewer loci
dataS <- dataS[seq(from=1, to=nrow(data), by=5),]

str(dataS)

gaps <- findLargeGaps(dataS, minLength=2e6)
knownSegments <- gapsToSegments(gaps)

# Paired PSCBS segmentation
fit <- segmentByPairedPSCBS(dataS, knownSegments=knownSegments,
                            seed=0xBEEF, verbose=-10)

# Fake a multi-chromosome segmentation
fit1 <- fit
fit2 <- renameChromosomes(fit, from=1, to=2)
fit <- append(fit1, fit2)

report(fit, sampleName="PairedPSCBS", studyName="PSCBS-Ex", verbose=-10)