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bioinfo
ngs_tools
Commits
86e140da
Commit
86e140da
authored
Sep 19, 2018
by
Lena Hersemann
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removed empty default for --out (files prefix)
parent
351a906d
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dge_workflow/featcounts_deseq_mf.R
dge_workflow/featcounts_deseq_mf.R
+2
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dge_workflow/featcounts_deseq_mf.R
View file @
86e140da
...
...
@@ -35,7 +35,7 @@ Options:
--qcutoff <qcutoff> Use a q-value cutoff of 0.01 instead of a q-value cutoff [default: 0.01]
--pcutoff <pcutoff> Override q-value filter and filter by p-value instead
--min_count <min_count> Minimal expression in any of the sample to be included in the final result list [default: 10]
--out <name_prefix> Name to prefix all generated result files
[default: ]
--out <name_prefix> Name to prefix all generated result files
--design <formula> Design fomula for DeSeq with contrast attribute at the end [default: condition]
--lfc <lfc_cutoff> Just report genes with abs(lfc) > lfc_cutoff as hits [default: 1.0]
--ensembl_db <ensembl_db> Ensebmbl db to be used. If not specified inferred from data. TODO implement NONE here!!
...
...
@@ -75,7 +75,7 @@ sub_data = as.logical(opts$sub_data)
gene_info_file
=
opts
$
gene_info
assert
(
is.null
(
gene_info_file
)
||
file.exists
(
gene_info_file
),
"invalid gene_info_file"
)
resultsBase
=
if
(
str_length
(
opts
$
out
)
>
0
)
paste0
(
opts
$
out
,
"."
)
else
""
resultsBase
=
if
(
!
is.null
(
opts
$
out
)
)
paste0
(
opts
$
out
,
"."
)
else
""
pcutoff
=
if
(
is.null
(
opts
$
pcutoff
))
NULL
else
as.numeric
(
opts
$
pcutoff
)
qcutoff
=
if
(
is.numeric
(
pcutoff
))
NULL
else
as.numeric
(
opts
$
qcutoff
)
...
...
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