[Bioc-devel] Restrictions on findOverlaps parameters with SummarizedExperiment objects

Fri, Apr 11, 2014 1:45 PM

On 04/10/2014 11:44 PM, Peter Hickey wrote:

Hi Pete -- Updated in 1.15.46, thanks. I think the original rationale had been 
that the rowData can be a GRanges or GRangesList, and type and select are not 
equally supported across these types, so only those values implemented for all 
row data were available. Martin

Thanks,
Pete

These examples use GenomicRanges_1.14.4:

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
## Returns error: "Error in match.arg(type) :   'arg' should be one of "any", "start", "end", "within""
nrows <- 200; ncols <- 6
   counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
   rowData <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
                      IRanges(floor(runif(200, 1e5, 1e6)), width=100),
                      strand=sample(c("+", "-"), 200, TRUE))
   colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
                        row.names=LETTERS[1:6])
   sset <- SummarizedExperiment(assays=SimpleList(counts=counts),
                  rowData=rowData, colData=colData)
findOverlaps(sset, sset, type = 'equal')

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
## But this works fine (ostensibly doing the same thing as the above but via a different signature)
findOverlaps(sset, rowData(sset), type = 'equal')

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
## I looked at the method definitions for various signatures
## This revealed that only a subset of "type" and "select" arguments are allowed for certain signatures involving SummarizedExperiment objects
## E.g. Does not allow type = 'equal' or select = 'last' or select = 'arbitrary'
selectMethod('findOverlaps', c('SummarizedExperiment', 'SummarizedExperiment'))
Method Definition:

function (query, subject, maxgap = 0L, minoverlap = 1L, type = c("any",
     "start", "end", "within"), select = c("all", "first"), ...)
{
     .local <- function (query, subject, maxgap = 0L, minoverlap = 1L,
         type = c("any", "start", "end", "within"), select = c("all",
             "first"), ignore.strand = FALSE)
     {
         findOverlaps(rowData(query), rowData(subject), maxgap = maxgap,
             minoverlap = minoverlap, type = match.arg(type),
             select = match.arg(select), ignore.strand = ignore.strand)
     }
     .local(query, subject, maxgap, minoverlap, type, select,
         ...)
}
<environment: namespace:GenomicRanges>

Signatures:
         query                  subject
target  "SummarizedExperiment" "SummarizedExperiment"
defined "SummarizedExperiment" "SummarizedExperiment"

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
## E.g. Does allow type = 'equal' but does not allow select = 'last' or select = 'arbitrary'
selectMethod('findOverlaps', c('SummarizedExperiment', 'Vector'))
Method Definition:

function (query, subject, maxgap = 0L, minoverlap = 1L, type = c("any",
     "start", "end", "within", "equal"), select = c("all", "first"),
     ...)
{
     .local <- function (query, subject, maxgap = 0L, minoverlap = 1L,
         type = c("any", "start", "end", "within", "equal"), select = c("all",
             "first"), ignore.strand = FALSE)
     {
         findOverlaps(rowData(query), subject, maxgap = maxgap,
             minoverlap = minoverlap, type = match.arg(type),
             select = match.arg(select), ignore.strand = ignore.strand)
     }
     .local(query, subject, maxgap, minoverlap, type, select,
         ...)
}
<environment: namespace:GenomicRanges>

Signatures:
         query                  subject
target  "SummarizedExperiment" "Vector"
defined "SummarizedExperiment" "Vector"

### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
## E.g. Does allow type = 'equal' but does not allow select = 'last' or select = 'arbitrary'
selectMethod('findOverlaps', c('Vector', 'SummarizedExperiment'))
Method Definition:

function (query, subject, maxgap = 0L, minoverlap = 1L, type = c("any",
     "start", "end", "within", "equal"), select = c("all", "first"),
     ...)
{
     .local <- function (query, subject, maxgap = 0L, minoverlap = 1L,
         type = c("any", "start", "end", "within", "equal"), select = c("all",
             "first"), ignore.strand = FALSE)
     {
         findOverlaps(query, rowData(subject), maxgap = maxgap,
             minoverlap = minoverlap, type = match.arg(type),
             select = match.arg(select), ignore.strand = ignore.strand)
     }
     .local(query, subject, maxgap, minoverlap, type, select,
         ...)
}
<environment: namespace:GenomicRanges>

Signatures:
         query    subject
target  "Vector" "SummarizedExperiment"
defined "Vector" "SummarizedExperiment"

--------------------------------
Peter Hickey,
PhD Student/Research Assistant,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Ph: +613 9345 2324

hickey at wehi.edu.au
http://www.wehi.edu.au

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[Bioc-devel] Restrictions on findOverlaps parameters with SummarizedExperiment objects

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