Skip to content
Prev 313820 / 398503 Next

Code works standalone, yet same code fails when part of package

WATSON Mick 
Hi

I'm missing something here but I cannot figure out what.  What I can see is that the same code works when I load it via source(...) yet fails when I execute it after loading the package I have built (which includes the code.

Below is a transcript of my R session.  First I load the code from a file, using source().  Then I execute it fine.  Then I remove the function object, I load the package, and execute the same code from the package - and I get an error.

Please help!

Mick
function(bamfile=NULL, chr=NULL, start=1, end=1e07, what=c("qname",  "flag",   
"rname",  "strand", "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("DataFrame", lst)
        df <- df[!is.na(df$qwidth),]

        df$seq <- as.character(df$seq)
        df$cigar <- as.character(df$cigar)

        df$rname <- rep(chr, nrow(df))

        if (removeN==TRUE) {
                ns <- grep("N", df$seq)
                if (length(ns) > 0) {
                        df <- df[-ns,]
                }
        }

        return(as.data.frame(df))
}
Loading required package: seqinr

Attaching package: ?seqinr?

The following object(s) are masked from ?package:Biostrings?:

    translate

Loading required package: plyr

Attaching package: ?plyr?

The following object(s) are masked from ?package:seqinr?:

    count

The following object(s) are masked from ?package:IRanges?:

    compact, desc, rename

Loading required package: gsubfn
Loading required package: proto
Loading required namespace: tcltk
Loading Tcl/Tk interface ... done
Loading required package: seqLogo
Loading required package: grid
function (bamfile = NULL, chr = NULL, start = 1, end = 1e+07,
    what = c("qname", "flag", "rname", "strand", "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]])
    df <- do.call("DataFrame", lst)
    df <- df[!is.na(df$qwidth), ]
    df$seq <- as.character(df$seq)
    df$cigar <- as.character(df$cigar)
    df$rname <- rep(chr, nrow(df))
    if (removeN == TRUE) {
        ns <- grep("N", df$seq)
        if (length(ns) > 0) {
            df <- df[-ns, ]
        }
    }
    return(as.data.frame(df))
}
<environment: namespace:viRome>
Error in as.data.frame.default(df) :
  cannot coerce class 'structure("DataFrame", package = "IRanges")' into a 

data.frame

R version 2.15.2 (2012-10-26)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] viRome_0.2           seqLogo_1.24.0       gsubfn_0.6-5
 [4] proto_0.3-9.2        plyr_1.8             seqinr_3.0-7
 [7] Rsamtools_1.10.2     Biostrings_2.26.2    GenomicRanges_1.10.5
[10] IRanges_1.16.4       BiocGenerics_0.4.0

loaded via a namespace (and not attached):
[1] bitops_1.0-5    parallel_2.15.2 stats4_2.15.2   tcltk_2.15.2
[5] zlibbioc_1.4.0

Thread (2 messages)

WATSON Mick Code works standalone, yet same code fails when part of package Dec 17 Martin Morgan Code works standalone, yet same code fails when part of package Dec 17