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Armin Rauschenberger
joinet
Commits
0b461e54
Commit
0b461e54
authored
Jul 24, 2018
by
Rauschenberger
Browse files
automation
parent
d1cc60e6
Changes
3
Hide whitespace changes
Inline
Side-by-side
R/functions.R
View file @
0b461e54
...
...
@@ -911,6 +911,7 @@ test.multiple <- function(Y,X,map,rho=c(0,0.5,1),spec=1,steps=20){
limit
<-
ceiling
(
0.05
*
max
/
p
)
steps
<-
diff
(
limit
^
seq
(
from
=
1
,
to
=
log
(
max
)
/
log
(
limit
),
length.out
=
pmin
(
p
,
steps
)))
# was (p,20)
steps
<-
c
(
limit
,
round
(
steps
))
# Or replace "limit" by "minimum # of permutations"!
steps
[
steps
==
0
]
<-
1
steps
[
length
(
steps
)]
<-
max
-
sum
(
steps
[
-
length
(
steps
)])
}
...
...
docs/articles/vignette.html
View file @
0b461e54
...
...
@@ -195,7 +195,7 @@
<a
class=
"sourceLine"
id=
"cb5-10"
data-line-number=
"10"
>
</a>
<a
class=
"sourceLine"
id=
"cb5-11"
data-line-number=
"11"
>
<span
class=
"kw"
>
rm
</span>
(
<span
class=
"dt"
>
list=
</span><span
class=
"kw"
>
setdiff
</span>
(
<span
class=
"kw"
>
ls
</span>
(),
<span
class=
"kw"
>
c
</span>
(
<span
class=
"st"
>
"data"
</span>
,
<span
class=
"st"
>
"chr"
</span>
,
<span
class=
"st"
>
"path"
</span>
)));
<span
class=
"kw"
>
gc
</span>
();
<span
class=
"kw"
>
cat
</span>
(
<span
class=
"st"
>
"."
</span>
)
</a>
<a
class=
"sourceLine"
id=
"cb5-12"
data-line-number=
"12"
>
<span
class=
"kw"
>
load
</span>
(
<span
class=
"kw"
>
file.path
</span>
(path,
<span
class=
"kw"
>
paste0
</span>
(
<span
class=
"st"
>
"temp."
</span>
,data,
<span
class=
"st"
>
".chr"
</span>
,chr,
<span
class=
"st"
>
".RData"
</span>
)));
<span
class=
"kw"
>
cat
</span>
(
<span
class=
"st"
>
"."
</span>
)
</a>
<a
class=
"sourceLine"
id=
"cb5-13"
data-line-number=
"13"
>
pvalue
<
-
<span
class=
"st"
>
</span>
spliceQTL
<span
class=
"op"
>
::
</span><span
class=
"kw"
><a
href=
"http://www.rdocumentation.org/packages/spliceQTL/topics/test.multiple"
>
test.multiple
</a></span>
(
<span
class=
"dt"
>
Y=
</span>
exons,
<span
class=
"dt"
>
X=
</span>
snps,
<span
class=
"dt"
>
map=
</span>
map,
<span
class=
"dt"
>
rho=
</span><span
class=
"dv"
>
1
</span>
,
<span
class=
"dt"
>
spec=
</span><span
class=
"dv"
>
16
</span>
);
<span
class=
"kw"
>
cat
</span>
(
<span
class=
"st"
>
"."
</span>
)
</a>
<a
class=
"sourceLine"
id=
"cb5-13"
data-line-number=
"13"
>
pvalue
<
-
<span
class=
"st"
>
</span>
spliceQTL
<span
class=
"op"
>
::
</span><span
class=
"kw"
><a
href=
"http://www.rdocumentation.org/packages/spliceQTL/topics/test.multiple"
>
test.multiple
</a></span>
(
<span
class=
"dt"
>
Y=
</span>
exons,
<span
class=
"dt"
>
X=
</span>
snps,
<span
class=
"dt"
>
map=
</span>
map,
<span
class=
"dt"
>
rho=
</span><span
class=
"dv"
>
1
</span>
,
<span
class=
"dt"
>
spec=
</span><span
class=
"dv"
>
16
</span>
,
<span
class=
"dt"
>
steps=
</span><span
class=
"dv"
>
30
</span>
);
<span
class=
"kw"
>
cat
</span>
(
<span
class=
"st"
>
"."
</span>
)
</a>
<a
class=
"sourceLine"
id=
"cb5-14"
data-line-number=
"14"
>
<span
class=
"kw"
>
save
</span>
(
<span
class=
"dt"
>
object=
</span>
pvalue,
<span
class=
"dt"
>
file=
</span><span
class=
"kw"
>
file.path
</span>
(path,
<span
class=
"kw"
>
paste0
</span>
(
<span
class=
"st"
>
"pval."
</span>
,data,
<span
class=
"st"
>
".chr"
</span>
,chr,
<span
class=
"st"
>
".RData"
</span>
)));
<span
class=
"kw"
>
cat
</span>
(
<span
class=
"st"
>
"
</span><span
class=
"ch"
>
\n
</span><span
class=
"st"
>
"
</span>
)
</a>
<a
class=
"sourceLine"
id=
"cb5-15"
data-line-number=
"15"
>
}
</a>
<a
class=
"sourceLine"
id=
"cb5-16"
data-line-number=
"16"
><span
class=
"co"
>
#q()
</span></a>
...
...
vignettes/vignette.Rmd
View file @
0b461e54
...
...
@@ -131,7 +131,7 @@ for(chr in 22:1){
rm(list=setdiff(ls(),c("data","chr","path"))); gc(); cat(".")
load(file.path(path,paste0("temp.",data,".chr",chr,".RData"))); cat(".")
pvalue <- spliceQTL::test.multiple(Y=exons,X=snps,map=map,rho=1,spec=16); cat(".")
pvalue <- spliceQTL::test.multiple(Y=exons,X=snps,map=map,rho=1,spec=16
,steps=30
); cat(".")
save(object=pvalue,file=file.path(path,paste0("pval.",data,".chr",chr,".RData"))); cat("\n")
}
#q()
...
...
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