callsnvs: Call somatic SNVs by using both global and local error models
In abemus: Adaptive Base Error Model in Ultra-Deep Sequencing Data

Description Usage Arguments Value Examples

Call somatic SNVs by using both global and local error models

callsnvs(sample.info.file, outdir, targetbed,
  pbem_dir = file.path(outdir, "BaseErrorModel"),
  controls_dir = file.path(outdir, "Controls"), pacbamfolder_bychrom,
  detection.specificity = 0.995, replicas = 1000,
  replicas.in.parallel = 1, coeffvar.threshold = 0.01,
  AFbycov = TRUE, mincov = 10, mincovgerm = 10, minalt = 1,
  maxafgerm = 0.2, coverage_binning = 50,
  outdir.calls.name = "Results", chrom.in.parallel = 1)

`sample.info.file`	The sample info file listing CASE and CONTROL samples. The format is simply 5 columns, tab-delimited, and there is no column header.
`outdir`	The folder where outputs will be saved.
`targetbed`	Genomic regions in the BED tab-delimited format.
`pbem_dir`	The folder with outputs generated by the `compute_pbem` function. default: file.path(outdir, "BaseErrorModel")
`controls_dir`	The folder with outputs generated by the `compute_afthreshold` function. default: file.path(outdir, "Controls")
`pacbamfolder_bychrom`	The folder popluted by outputs by the `split_pacbam_bychrom` function.
`detection.specificity`	The quantile of the GSE distribution(s) to use to compute the AF threhold. default: 0.995
`replicas`	Replics sampling to define stability of AF threhold in bins of coverage. default: 1000
`replicas.in.parallel`	default: 1
`coeffvar.threshold`	Consider a bin as stable if the coefficient of variations after `replicas` is lower than the `coeffvar.threshold`. default: 0.01
`AFbycov`	Apply coverage-based AF threhold. default: TRUE
`mincov`	Minimum locus coverage in CASE sample. default: 10
`mincovgerm`	Minimum locus coverage in CONTROL sample. default: 10
`minalt`	Minimum number of reads supporting the alternative allele in CASE sample. default: 1
`maxafgerm`	Maximum allelic fraction observed in matched CONTROL locus. default: 0.2
`coverage_binning`	Bins of coverage into which divide AFs. default: 50
`outdir.calls.name`	The subfolder name that will be created in the `outdir`. default: "Results"
`chrom.in.parallel`	Number of chromosomes to run in parallel. default: 1

The callsnvs will create a subfolder for each CASE sample within the outdir.calls.name folder. There tab-delimeted files reporting SNV calls passing 3 consecutive filtering steps (pmtab_F1, pmtab_F2 and pmtab_F3) are saved.

The function also return the data.frame tabsnvs_index reeporting for each sample the path to each of the tables generated during the 3 filtering steps.

sample.info.file <- system.file("extdata", "test_sif_toy.tsv", package = "abemus")
outdir <- tempdir()
targetbed <- system.file("extdata", "regions_toy.bed", package = "abemus")
pacbamfolder_bychrom <- system.file("extdata", "pacbam_data_bychrom", package = "abemus")
pbem_dir <- system.file("extdata", "BaseErrorModel", package = "abemus")
controls_dir <- system.file("extdata", "Controls", package = "abemus")
callsnvs(sample.info.file,outdir,targetbed,pbem_dir,controls_dir,pacbamfolder_bychrom,replicas=1)