Hi,

I am following this vignette for transcriptR (https://bioconductor.org/packages/release/bioc/vignettes/transcriptR/inst/doc/transcriptR.pdf) an R package that combines RNA-seq and ChIP-seq data. The predictStrand feature combines the data contained within the RNA-seq and ChIP-seq data objects constructed earlier in the vignette.

predictStrand(cdsObj = cds, tdsObj = tds, quant.cutoff = 0.1, win.size = 2000)
cds
peaks <- getPeaks(cds)
head(peaks[ peaks$predicted.tssOverlap == "yes" ], 3)

Error:

 predictStrand(cdsObj = cds, tdsObj = tds, quant.cutoff = 0.1, win.size = 2000)
[INFO] Creating coverage profiles for the starts of the fragments...Done!
[IFNO] Estimating transcription start position...Error: subscript contains invalid names

Traceback:

Error: subscript contains invalid names
15.

stop(wmsg(...), call. = FALSE)
14.

.subscript_error("subscript contains invalid ", what)
13.

NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)
12.

NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)
11.

normalizeSingleBracketSubscript(i, x, as.NSBS = TRUE)
10.

extractROWS(x, i)
9.

extractROWS(x, i)
8.

subset_along_ROWS(x, i, drop = drop)
7.

cov.frags[chrs]
6.

cov.frags[chrs]
5.

lapply(names(cov.frags[chrs]), function(x) { Views(subject = cov.frags[[x]], start = start(peaks[seqnames(peaks) == x]), end = end(peaks[seqnames(peaks) == x])) })
4.

RleViewsList(lapply(names(cov.frags[chrs]), function(x) { Views(subject = cov.frags[[x]], start = start(peaks[seqnames(peaks) == x]), end = end(peaks[seqnames(peaks) == x])) }))
3.

.q1q2SeparatingLine(peaks = peaks, cov.frags = tdsObj@coveragePlus, cov.starts = cov.s.pls, cov.cutoff = coverage.cutoff, cum.cov.cutoff = quant.cutoff, strand = "+")
2.

predictStrand(cdsObj = cds, tdsObj = tds, quant.cutoff = 0.1, win.size = 2000)
1.

predictStrand(cdsObj = cds, tdsObj = tds, quant.cutoff = 0.1, win.size = 2000)

I can't find any informative solutions online, any help would be appreciated.

Best wishes,

Jason