PreProcSnpPileup: PreProcSnpPileup takes a snp-pileup generated pileup file and...
In rptashkin/facets2n: Cellular Faction and Copy Numbers from Tumor Sequencing
View source: R/facets-procreads.R
PreProcSnpPileup R Documentation
PreProcSnpPileup takes a snp-pileup generated pileup file and process it into a data frame format for downstream processing.
Description
PreProcSnpPileup takes a snp-pileup generated pileup file and process it into a data frame format for downstream processing.
Usage
PreProcSnpPileup(
filename,
err.thresh = Inf,
del.thresh = Inf,
is.Reference = FALSE,
gbuild = "hg19"
)
Arguments
filename
(character) File path to snp-pileup generated pileup file.
err.thresh
(numeric) Error threshold to be used to filter snp-pileup data frame.
del.thresh
(numeric) Deletion threshold to be used to filter snp-pileup data frame.
is.Reference
(logical) Indicate whether the snp-pilep is Reference data.
gbuild
(character) genome build version.
Value
A data drame of pileup depth values filtered against del.thresh and err.thresh values.
rptashkin/facets2n documentation built on May 11, 2022, 1:34 p.m.
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View source: R/facets-procreads.R
| PreProcSnpPileup | R Documentation |
PreProcSnpPileup takes a snp-pileup generated pileup file and process it into a data frame format for downstream processing.
Description
PreProcSnpPileup takes a snp-pileup generated pileup file and process it into a data frame format for downstream processing.
Usage
PreProcSnpPileup( filename, err.thresh = Inf, del.thresh = Inf, is.Reference = FALSE, gbuild = "hg19" )
Arguments
filename |
(character) File path to snp-pileup generated pileup file. |
err.thresh |
(numeric) Error threshold to be used to filter snp-pileup data frame. |
del.thresh |
(numeric) Deletion threshold to be used to filter snp-pileup data frame. |
is.Reference |
(logical) Indicate whether the snp-pilep is Reference data. |
gbuild |
(character) genome build version. |
Value
A data drame of pileup depth values filtered against del.thresh and err.thresh values.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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