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Debian R Packages Maintainers
r-bioc-summarizedexperiment
Commits
122fd1b6
Commit
122fd1b6
authored
6 years ago
by
Andreas Tille
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New upstream version 1.10.1
parent
fb309692
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DESCRIPTION
+2
-2
2 additions, 2 deletions
DESCRIPTION
R/RangedSummarizedExperiment-class.R
+24
-17
24 additions, 17 deletions
R/RangedSummarizedExperiment-class.R
with
26 additions
and
19 deletions
DESCRIPTION
+
2
−
2
View file @
122fd1b6
...
...
@@ -4,7 +4,7 @@ Description: The SummarizedExperiment container contains one or more assays,
each represented by a matrix-like object of numeric or other mode.
The rows typically represent genomic ranges of interest and the columns
represent samples.
Version: 1.10.
0
Version: 1.10.
1
Encoding: UTF-8
Author: Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
...
...
@@ -27,4 +27,4 @@ Collate: Assays-class.R SummarizedExperiment-class.R
makeSummarizedExperimentFromDataFrame.R
makeSummarizedExperimentFromLoom.R readKallisto.R zzz.R
NeedsCompilation: no
Packaged: 2018-05-
0
1 00:2
8:59
UTC; biocbuild
Packaged: 2018-05-
1
1 00:2
9:37
UTC; biocbuild
This diff is collapsed.
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R/RangedSummarizedExperiment-class.R
+
24
−
17
View file @
122fd1b6
...
...
@@ -126,24 +126,31 @@ setMethod("SummarizedExperiment", "SimpleList",
}
}
## validate
ok
<-
vapply
(
assays
,
function
(
x
)
{
colnames
<-
colnames
(
x
)
test
<-
is.null
(
colnames
)
||
identical
(
colnames
,
ans_colnames
)
if
(
!
test
)
stop
(
"assay colnames() must be NULL or equal colData rownames()"
)
rownames
<-
rownames
(
x
)
test
<-
test
&&
is.null
(
rownames
)
||
identical
(
rownames
,
ans_rownames
)
if
(
!
test
)
{
txt
<-
"assay rownames() must be NULL or equal rowData rownames() /
rowRanges names()"
stop
(
paste
(
strwrap
(
txt
,
exdent
=
2
),
collapse
=
"\n"
))
}
## validate the assay rownames and colnames
.validate_names
<-
function
(
nms
,
expected_nms
,
what1
,
what2
)
{
if
(
is.null
(
nms
))
return
()
if
(
!
is.character
(
nms
))
stop
(
wmsg
(
what1
,
" must be NULL or a character vector"
))
if
(
!
is.null
(
attributes
(
nms
)))
stop
(
wmsg
(
what1
,
" must be NULL or a character vector"
,
" with no attributes"
))
if
(
!
identical
(
nms
,
expected_nms
))
stop
(
wmsg
(
what1
,
" must be NULL or identical to "
,
what2
))
}
test
},
logical
(
1
))
for
(
i
in
seq_along
(
assays
))
{
a
<-
assays
[[
i
]]
rownames
<-
rownames
(
a
)
.validate_names
(
rownames
,
ans_rownames
,
"assay rownames()"
,
"rowData rownames() / rowRanges names()"
)
colnames
<-
colnames
(
a
)
.validate_names
(
colnames
,
ans_colnames
,
"assay colnames()"
,
"colData rownames()"
)
}
assays
<-
Assays
(
assays
)
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