On 04/10/2014 11:44 PM, Peter Hickey wrote:
Could the findOverlaps method with signatures involving SummarizedExperiment objects please be extended to allow the full range of "type" and "select" arguments"? Please see the examples below for situations where the parameter choices seem unduly restrictive. Are there reasons for these restrictions?
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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