camelTest
(Package: ampliQueso) :
camelTest - calculating permutation tests for camel measures (sequential and parallel versions)
Calculating permutation tests for reads coverage (camel) measures for regions specified by a BED file. This function features a few normalization modes and camel measures.
● Data Source:
BioConductor
● Keywords:
● Alias: camelTest
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compareCoverages
(Package: ampliQueso) :
compareCoverages - camel measure for a single comparison.
Comparing coverage profiles with the camel measures for the two groups of BAM files, for a given genomic region.
● Data Source:
BioConductor
● Keywords:
● Alias: compareCoverages
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compareCoveragesReg
(Package: ampliQueso) :
compareCoveragesReg - calculating given camel measures for a list of regions specified by a BED file (sequential and parallel versions)
Calculating given camel measures for a list of regions specified by a BED file (sequential version)
● Data Source:
BioConductor
● Keywords:
● Alias: compareCoveragesReg
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getCountTable
(Package: ampliQueso) :
getCountTable - obtaining typical count table.
Obtaining a count table for all the amplicons described in the BED file.
● Data Source:
BioConductor
● Keywords:
● Alias: getCountTable
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getSNP
(Package: ampliQueso) :
getSNP - finding SNPs in all samples for regions specified by a BED file all regions if BED file not provided (sequential and parallel versions)
Finding SNPs in all samples for regions specified by a BED file (sequential version) using Samtools mpileup functionality. Please make sure that samtools executables are installed and available from command line without specifing the full path(e.g. added to the PATH environment variable)
● Data Source:
BioConductor
● Keywords:
● Alias: getSNP
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runAQReport
(Package: ampliQueso) :
runAQReport - runing the AmpliQueso report
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.
● Data Source:
BioConductor
● Keywords:
● Alias: runAQReport
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