applyTallies
(Package: h5vc) :
Preparing the results of tallyBAM for writing to an HDF5 tally file
This function tallies a set of bam files and prepares the data for writing to an HDF5 tally file.
● Data Source:
BioConductor
● Keywords:
● Alias: applyTallies
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batchTallies
(Package: h5vc) :
Tallying bam files in parallel using code{BatchJobs
These function tally a set of bam files in blocks spanning a specified region and write the results to an HDF5 tally file; uses BatchJobs for parallel computation on HPCs
● Data Source:
BioConductor
● Keywords:
● Alias: batchTallies, batchTallyParam, collectTallies, rerunBatchTallies
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Function for generating a GRanges representation of a binning of the genome given in the reference object.
● Data Source:
BioConductor
● Keywords:
● Alias: binGenome
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This function is used to give estimates of the ditribution of observed allelic freuqencies in a regions of the genome, use in conjunction with h5dapply
● Data Source:
BioConductor
● Keywords:
● Alias: binnedAFs
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These functions implement various attempts at variant calling.
● Data Source:
BioConductor
● Keywords:
● Alias: callDeletionsPaired, callVariantsPaired, vcConfParams
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callVariantsFisher
(Package: h5vc) :
Paired variant calling using fisher tests
This function implements a simple paired variant calling strategy based on the fisher test
● Data Source:
BioConductor
● Keywords:
● Alias: callVariantsPairedFisher
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A simple single sample variant calling function (calling SNVs and deletions)
● Data Source:
BioConductor
● Keywords:
● Alias: callVariantsSingle
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Coverage
(Package: h5vc) :
Coverage analysis
Functions to do analyses based on coverage
● Data Source:
BioConductor
● Keywords:
● Alias: binnedCoverage
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Plotting function that returns a ggplot2 layer representing the specified dataset for the specified samples in the region [positon - windowsize, position + windowsize].
● Data Source:
BioConductor
● Keywords:
● Alias: geom_h5vc
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getSampleData
(Package: h5vc) :
Reading and writing sample data from / to a tally file
These functions allow reading and writing of sample data to the HDF5-based tally files. The sample data is stored as group attribute.
● Data Source:
BioConductor
● Keywords:
● Alias: getSampleData, setSampleData
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