runAQReport - runing the AmpliQueso report

Share:

Description

This function creates AmpliQueso report in PDF format using either Article or Beamer LaTeX document classes. Report is created in current working directory. Please make sure that you have Beamer LaTeX package installed prior to running this report if you choose this output report type.

Usage

1
runAQReport(iCovdesc, iBedFile, iRefSeqFile, iGroup, iT1, iT2, iTopN = 5, iMinQual, iReportFormat = "pdf", iReportType = "article",iReportPath="", iVerbose = TRUE, iVCF = NULL, iParallel=TRUE)

Arguments

iCovdesc

Covdesc-like data frame - BAM files are read from row names. Similar to covdesc in simpleaffy and rnaSeqMap - tab delimited table of BAM files and groupings. This is the table of experimental design.

iBedFile

BED file with same genomic coordinates as in BAMs (preferably standard hg19)

iRefSeqFile

Reference sequence in FASTA format used for SNPs detection. If set to NULL (by default) will skip SNP report.

iGroup

Name of the attribute/group in the experimental description (i.e. covdesc)

iT1

name of the first group from the experiment (it should be consistent with the groupings specified in covdesc file)

iT2

name of the other group from the experiment (it should be consistent with the groupings specified in covdesc file)

iTopN

number specifing top n expressed genes to be reported

iMinQual

number specifing the minimum quality of the SNPs returned by samtools used to filter out these of poor quality. Please refer to Samtools documentation for further details on the definition of this measure.

iReportFormat

Report output format. Currently PDF only.

iReportType

LaTeX document class to be used for report generation.

iReportPath

Output path for the report. It is created in the current working directory by default.

iVerbose

Boolean specifing whether R code should be inlcude in the report, if set to FALSE only figures and tables will be included.

iVCF

TBD

iParallel

Boolean specifing whether R code should be run in parallel – it is turned on by default..

Value

No vaue returned.

Author(s)

Alicja Szabelska, Marek Wiewiorka, Michal Okoniewski

Examples

1
#runAQReport(iCovdesc="covdesc",iBedFile="test.BED",iRefSeqFile=NULL,iGroup="group",iT1="sick",iT2="healthy",iTopN=5,iMinQual=10,iReportFormat="pdf",iReportType="article",iVerbose=FALSE,iVCF=NULL)