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shaman
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Amine GHOZLANE
shaman
Commits
3f77e0b2
Commit
3f77e0b2
authored
Sep 25, 2019
by
Amine GHOZLANE
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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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2 changed files
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3 additions
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2 deletions
+3
-2
Rfunctions/DiagPlot.R
Rfunctions/DiagPlot.R
+1
-1
Rfunctions/Stat_Model.R
Rfunctions/Stat_Model.R
+2
-1
No files found.
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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