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Amine GHOZLANE
shaman
Commits
3f77e0b2
Commit
3f77e0b2
authored
Sep 25, 2019
by
Amine GHOZLANE
Browse files
Debug DESeq worker when the data are large and we want to expand the contrast
parent
310bfc18
Pipeline
#15159
passed with stage
in 8 minutes and 17 seconds
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2
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Rfunctions/DiagPlot.R
View file @
3f77e0b2
...
...
@@ -413,7 +413,7 @@ PCoAPlot_meta <-function (input, dds, group_init, CT,tree,col = c("SpringGreen",
## Get the group corresponding to the modalities
group
=
group
[
ind_kept
]
nb
=
length
(
unique
((
group
)))
group
=
as.
factor
(
group
)
group
=
factor
(
group
,
levels
=
Kval
)
if
(
nlevels
(
group
)
!=
0
&&
!
is.null
(
input
$
PCaxe1
)
&&
!
is.null
(
input
$
PCaxe2
))
{
...
...
Rfunctions/Stat_Model.R
View file @
3f77e0b2
...
...
@@ -63,7 +63,8 @@ Get_dds_object <- function(input,counts,target,design,normFactorsOTU,CT_noNorm,C
# dds <- nbinomWaldTest(dds,modelMatrixType = "expanded")
if
(
nrow
(
counts
)
*
nrow
(
target
)
>=
50000
)
{
dds
=
DESeq2shaman
::
DESeq
(
dds
,
fitType
=
input
$
fitType
,
parallel
=
TRUE
,
minReplicatesForReplace
=
Inf
,
modelMatrixType
=
"expanded"
)
dds
=
DESeq2shaman
::
DESeq
(
dds
,
test
=
"Wald"
,
fitType
=
input
$
fitType
,
parallel
=
TRUE
,
minReplicatesForReplace
=
Inf
,
modelMatrixType
=
"expanded"
)
#
# try(DESeq(dds,fitType=input$fitType,parallel = TRUE,minReplicatesForReplace = Inf) ->ddstmp,silent = TRUE)
# if(!is.null(ddstmp)) dds = ddstmp
}
...
...
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