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pneuvial / c3co

Inferring cancer cell clonality from copy-number data
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ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [data.frame] #77

Open HenrikBengtsson opened 4 years ago

HenrikBengtsson commented 4 years ago 
$ for pkg in $pkgs; do echo "$pkg:"; (cd "$pkg"; grep -E "^[ \t]*[^#].*data[.]frame" -- */*.R | grep -vF stringsAsFactors;); echo; read -r -p "Press ENTER to continue ..."; done

c3co:
R/AllGenerics.R:            datCC <- data.frame(chr=cc, start=start, arch=arch, end=end, CopyNumber=Z, stat=vv)
R/buildSubclones.R:        datAB <- data.frame(ct=dat$c, baft=dat$b, genotype=1/2, region=regz,
R/buildSubclones.R:        datAA <- data.frame(ct=dat$c, baft=dat$b, genotype=0, region=regz,
R/buildSubclones.R:        datBB <- data.frame(ct=dat$c, baft=dat$b, genotype=1, region=regz,
R/buildSubclones.R:        dataAnnot <- data.frame(dataAnnotTP[, keepCols],
R/c3co.R:                stop("Each data.frame in 'dat' should have the same size")
R/Facetswrapper.R:        df <- data.frame(chr=dat$chrom, pos=dat$maploc)
R/fitC3co.R:    bestConfigp <- as.data.frame(bestConfigp)
R/fitC3co.R:    allConfig <- as.data.frame(allConfig)
R/heatmap.3.R:    retval$colorTable <- data.frame(low = retval$breaks[-length(retval$breaks)],
R/initializeZt.R:            t(sapply(split(as.data.frame(Y), f=cluster), FUN=colMeans))
R/mixSubclone.R:        data.frame(c1=c1, c2=c2, tcn=tcn, dh=dh,
R/PSCBSwrapper.R:        as.data.frame(df)