Thanks,
Pete
These examples use GenomicRanges_1.14.4:
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## 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')
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## But this works fine (ostensibly doing the same thing as the above but via a
different signature)
findOverlaps(sset, rowData(sset), type = 'equal')
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## 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"
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## 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
hic...@wehi.edu.au
http://www.wehi.edu.au
______________________________________________________________________
The information in this email is confidential and inte...{{dropped:16}}
