Displaying 3 results from an estimated 3 matches for "scanbamparam".
2012 Dec 17
1
Code works standalone, yet same code fails when part of package
...pos", "qwidth", "mapq", "cigar", "mrnm", "mpos",
"isize", "seq"), tag=c("NM"), removeN=TRUE) {
which <- RangesList(chr = IRanges(start,end))
names(which) <- chr
param <- ScanBamParam(which = which, what = what, tag=tag)
bam <- scanBam(bamfile, param=param)
lst <- lapply(names(bam[[1]]), function(elt) {do.call(c, unname(lapply
(bam, "[[", elt)))})
names(lst) <- names(bam[[1]])
# convert to data.frame
df <- do.call...
2010 Oct 14
0
GridR error
...QLite_0.9-2 rtracklayer_1.8.1 tools_2.11.1
Thanks,
Elizabeth
The full grid.input.Parameters:
Browse[1]> grid.input.Parameters
[1] " <anonymous>: no visible global function definition for
?myreadPairedAlignments?\n <anonymous>: no visible global function
definition for ?ScanBamParam?\n <anonymous>: no visible global function
definition for ?scanBamFlag?\n <anonymous>: no visible global function
definition for ?matchBamToNames?\n <anonymous>: no visible binding for
global variable ?GRangesList?\n <anonymous>: no visible binding for
global variable ?a...
2010 Oct 15
0
nomianl response model
...QLite_0.9-2 rtracklayer_1.8.1 tools_2.11.1
Thanks,
Elizabeth
The full grid.input.Parameters:
Browse[1]> grid.input.Parameters
[1] " <anonymous>: no visible global function definition for
?myreadPairedAlignments?\n <anonymous>: no visible global function
definition for ?ScanBamParam?\n <anonymous>: no visible global function
definition for ?scanBamFlag?\n <anonymous>: no visible global function
definition for ?matchBamToNames?\n <anonymous>: no visible binding for
global variable ?GRangesList?\n <anonymous>: no visible binding for
global variable ?a...