callVariants {h5vc} | R Documentation

## Variant calling

### Description

These functions implement various attempts at variant calling.

### Usage

    callVariantsPaired( data, sampledata, cl = vcConfParams() )

    vcConfParams(
      minStrandCov = 5,
      maxStrandCov = 200,
      minStrandAltSupport = 2,
      maxStrandAltSupportControl = 0,
      minStrandDelSupport = minStrandAltSupport,
      maxStrandDelSupportControl = maxStrandAltSupportControl,
      minStrandInsSupport = minStrandAltSupport,
      maxStrandInsSupportControl = maxStrandAltSupportControl,
      minStrandCovControl = 5,
      maxStrandCovControl = 200,
      bases = 5:8,
      returnDataPoints = TRUE,
      annotateWithBackground = TRUE,
      mergeCalls = TRUE,
      mergeAggregator = mean,
      pValueAggregator = max
    )

### Arguments

`data` | A `list` with elements `Counts` (a 4d `integer` array of size [1:12, 1:2, 1:k, 1:n]), `Coverage` (a 3d `integer` array of size [1:2, 1:k, 1:n]), `Deletions` (a 3d `integer` array of size [1:2, 1:k, 1:n]), `Reference` (a 1d `integer` vector of size [1:n]) – see Details.
`sampledata` | A `data.frame` with `k` rows (one for each sample) and columns `Type`, `Column` and (`SampleGroup` or `Patient`). The tally file should contain this information as a group attribute, see `getSampleData` for an example.
`cl` | A list with parameters used by the variant calling functions. Such a list can be produced, for instance, by a call to `vcConfParams`.
`minStrandCov` | Minimum coverage per strand in the case sample.
`maxStrandCov` | Maximum coverage per strand in the case sample.
`minStrandCovControl` | Minimum coverage per strand in the control sample.
`maxStrandCovControl` | Maximum coverage per strand in the control sample.
`minStrandAltSupport` | Minimum support for the alternative allele per strand in the case sample. This should be 1 or higher.
`maxStrandAltSupportControl` | Maximum support for the alternative allele per strand in the control sample. This should usually be 0.
`minStrandDelSupport` | Minimum support for the deletion per strand in the case sample. This should be 1 or higher.
`maxStrandDelSupportControl` | Maximum support for the deletion per strand in the control sample. This should usually be 0.
`minStrandInsSupport` | Minimum support for the insertion per strand in the case sample. This should be 1 or higher.
`maxStrandInsSupportControl` | Maximum support for the insertion per strand in the control sample. This should usually be 0.
`bases` | Indices for subsetting in the bases dimension of the Counts array, 5:8 extracts only those calls made in the middle one of the sequencing cycle bins.
`returnDataPoints` | Boolean flag to specify that a data.frame with the variant calls should be returned, otherwise only position are returned as a numeric vector. If `returnDataPoints == FALSE` only the variant positions are returned.
`annotateWithBackground` | Boolean flag to specify that the background mismatch / deletion frequency estimated from all control samples in the cohort should be added to the output. A simple binomial test will be performed as well. Only usefull if `returnDataPoints == TRUE`
`mergeCalls` | Boolean flag to specify that adjacent calls should be merged where appropriate (used by `callDeletionsPaired`). Only usefull applied if `returnDataPoints == TRUE`
`mergeAggregator` | Aggregator function for merging adjacent calls, defaults to `mean`, which means that a deletion larger than 1bp will be annotated with the means of the counts and coverages
`pValueAggregator` | Aggregator function for combining the p-values of adjacent calls when merging, defaults to `max`. Is only applied if `annotateWithBackground == TRUE`

### Details

`data` is a list of datasets which has to at least contain the `Counts` and `Coverages` for variant calling respectively `Deletions` for deletion calling. This list will usually be generated by a call to the `h5dapply` function in which the tally file, chromosome, datasets and regions within the datasets would be specified. See `?h5dapply` for specifics. In order for `callVariantsPaired` to return the correct locations of the variants there must be the `h5dapplyInfo` slot present in `data` as well. This is itself a list (being automatically added by `h5dapply` and `h5readBlock` respectively) and contains the slots `Group` (location in the HDF5 file) and `Blockstart`, which are used to set the chromosome and the genomic positions of variants.

`vcConfParams` is a helper function that builds a set of variant calling parameters as a list. This list is provided to the calling functions e.g. `callVariantsPaired` and influences their behavior.

`callVariantsPaired` implements a simple pairwise variant callign approach applying the filters specified in `cl`, and might additionally computes an estimate of the background mismatch rate (the mean mismatch rate of all samples labeled as 'Control' in the `sampledata` and annotate the calls with p-values for the `binom.test` of the observed mismatch counts and coverage at each of the samples labeled as 'Case'.

### Value

The result is either a list of positions with SNVs / deletions or a `data.frame` containing the calls themselves which might contain annotations. Adjacent calls might be merged and calls might be annotated with p-values depending on configuration parameters.

When the configuration parameter `returnDataPoints` is `FALSE` the functions return the positions of potential variants as a list containing one integer vector of positions for each sample, if no positions were found for a sample the list will contain `NULL` instead. In the case of `returnDatapoints == TRUE` the functions return either `NULL` if no poisitions were found or a `data.frame` with the following slots:

`Chrom` | The chromosome the potential variant / deletion is on
`Start` | The starting position of the variant / deletion
`End` | The end position of the variant / deletions (equal to Start for SNVs and single basepair deletions)
`Sample` | The `Case` sample in which the variant was observed
`altAllele` | The alternate allele for SNVs (skipped for deletions, would be `"-"`)
`refAllele` | The reference allele for SNVs (skipped for deletions since the tally file might not contain all the information necessary to extract it)
`caseCountFwd` | Support for the variant in the `Case` sample on the forward strand
`caseCountRev` | Support for the variant in the `Case` sample on the reverse strand
`caseCoverageFwd` | Coverage of the variant position in the `Case` sample on the forward strand
`caseCoverageRev` | Coverage of the variant position in the `Case` sample on the reverse strand
`controlCountFwd` | Support for the variant in the `Control` sample on the forward strand
`controlCountRev` | Support for the variant in the `Control` sample on the reverse strand
`controlCoverageFwd` | Coverage of the variant position in the `Control` sample on the forward strand
`controlCoverageRev` | Coverage of the variant position in the `Control` sample on the reverse strand

If the `annotateWithBackground` option is set the following extra columns are returned

`backgroundFrequencyFwd` | The averaged frequency of mismatches / deletions at the position of all samples of type `Control` on the forward strand
`backgroundFrequencyRev` | The averaged frequency of mismatches / deletions at the position of all samples of type `Control` on the reverse strand
`pValueFwd` | The `p.value` of the test `binom.test( caseCountFwd, caseCoverageFwd, p = backgroundFrequencyFwd, alternative = "greater")`
`pValueRev` | The `p.value` of the test `binom.test( caseCountRev, caseCoverageRev, p = backgroundFrequencyRev, alternative = "greater")`

The function `callDeletionsPaired` merges adjacent single-base deletion calls if the option `mergeCalls` is set to `TRUE`, in that case the counts and coverages ( e.g. `caseCountFwd` ) are aggregated using the function supplied in the `mergeAggregator` option of the configuration list (defaults to `mean`) and the p-values `pValueFwd` and `pValueFwd` (if `annotateWithBackground` is `TRUE`), are aggregated using the function supplied in the `pValueAggregator` option (defaults to `max`).

### Author(s)

Paul Pyl

### Examples

      library(h5vc) # loading library
      tallyFile <- system.file( "extdata", "example.tally.hfs5", package = "h5vcData" )
      sampleData <- getSampleData( tallyFile, "/ExampleStudy/16" )
      position <- 29979629
      windowsize <- 1000
      vars <- h5dapply( # Calling Variants
        filename = tallyFile,
        group = "/ExampleStudy/16",
        blocksize = 500,
        FUN = callVariantsPaired,
        sampledata = sampleData,
        cl = vcConfParams(returnDataPoints=TRUE),
        names = c("Coverages", "Counts", "Reference", "Deletions"),
        range = c(position - windowsize, position + windowsize)
      )
      vars <- do.call( rbind, vars ) # merge the results from all blocks by row
      vars # We did find a variant

[Package h5vc version 2.28.0 Index]