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Using dplyr::bind_rows() instead of dplyr::rbind_all() #1

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Using dplyr::bind_rows() instead of dplyr::rbind_all() #1

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e947319
Update DESCRIPTION
romainfrancois Oct 7, 2019
f18c5a5
Update NAMESPACE
romainfrancois Oct 7, 2019
21e0f8e
Update rariantFromBam.R
romainfrancois Oct 7, 2019
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -4,7 +4,7 @@ Title: Identification and Assessment of Single Nucleotide Variants through Shift
Version: 1.7.1
Author: Julian Gehring, Simon Anders, Bernd Klaus (EMBL Heidelberg)
Maintainer: Julian Gehring <[email protected]>
Imports: methods, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, ggbio, ggplot2, exomeCopy, SomaticSignatures, Rsamtools, shiny, VGAM, dplyr, reshape2
Imports: methods, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, ggbio, ggplot2, exomeCopy, SomaticSignatures, Rsamtools, shiny, VGAM, dplyr (>= 0.5.0), reshape2
Depends: R (>= 3.0.2), GenomicRanges, VariantAnnotation
Suggests: h5vcData, testthat, knitr, optparse, BSgenome.Hsapiens.UCSC.hg19
Description: The 'Rariant' package identifies single nucleotide variants from sequencing data based on the difference of binomially distributed mismatch rates between matched samples.
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2 changes: 1 addition & 1 deletion NAMESPACE
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Expand Up @@ -12,7 +12,7 @@ importFrom(VariantAnnotation, VRanges)
importFrom(exomeCopy, subdivideGRanges)
importFrom(SomaticSignatures, seqchar)
importFrom(VGAM, logit)
importFrom(dplyr, rbind_all)
importFrom(dplyr, bind_rows)
importFrom(reshape2, melt)

export(acCi, nhsCi)
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2 changes: 1 addition & 1 deletion R/rariantFromBam.R
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Expand Up @@ -47,7 +47,7 @@ rariantFromBam <- function(test, control, region, beta = 0.95, alpha = 1 - beta,

res = NULL ## must be set
if(value & length(val) > 0) {
res = rbind_all(val) ## or unlist on a GRL
res = bind_rows(val) ## or unlist on a GRL
#if(!is.null(res)) { ## TODO: needed?
res = df2gr(res)
#}
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