preprocessData {CSSQ} | R Documentation |
This is a wrapper function that calls the functions to preprocess the data.
It results in a
RangedSummarizedExperiment-class
object
normalized counts and meta data that can be used by
DBAnalyze
.
preprocessData( inputRegions, sampleInfoFile, sampleDir = ".", inputCountData, numClusters = 4, noNeg = TRUE, plotDataToPDF = FALSE, ... )
inputRegions |
A bed file the regions to analyze. |
sampleInfoFile |
A tab separated file all sample information. The following are the columns that are present in the file. * Sample Name : Names for the samples. * Group : The group the sample belongs. * IP : The name of the sample bam file. * IP_aligned_reads : The number of aligned reads in the sample. This is used in depth normalization process. * IN : The name of the sample's control bam file. * IN_aligned_reads : The number of aligned reads in the control file. This is used in depth normalization process. |
sampleDir |
Location of the input sample files in 'sampleInfoFile' file. (default: ".") Name,Group/Label,IP bam location,IP number of reads,IN bam location, IN number of reads). |
inputCountData |
The path to the file count data. This parameter is used when directly loading count data from a file. This should be a tab separated file sample names as header. |
numClusters |
A numerical parameter indicating the number of clusters
to use in the normalization step. Passed on to |
noNeg |
A logical parameter indicating how to deal negative
values. It is passed to |
plotDataToPDF |
A logical parameter indicating whether to make plots of the
data distribution to a separate PDF file for each sample.
It is passed on to passed to |
... |
Additional arguments passed on to |
RangedSummarizedExperiment-class
containing the normalized counts, cluster information, the variance of the
cluster in the sample and metadata.
getRegionCounts
, ansTransform
and
normalizeData
which this function calls
processedData <- preprocessData(system.file("extdata", "chr19_regions.bed", package="CSSQ"),system.file("extdata", "sample_info.txt", package="CSSQ"), sampleDir = system.file("extdata", package="CSSQ"), numClusters=4,noNeg=TRUE,plotDataToPDF=FALSE) processedData