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Armin Rauschenberger
joinet
Commits
81c97798
Commit
81c97798
authored
Jul 17, 2018
by
Rauschenberger
Browse files
automation
parent
985a6b27
Changes
3
Hide whitespace changes
Inline
Side-by-side
R/functions.R
View file @
81c97798
...
...
@@ -837,6 +837,10 @@ test.single <- function(Y,X,map,i,limit=NULL,steps=NULL,rho=c(0,0.5,1)){
#' correlation\strong{:}
#' numeric vector with values between \eqn{0} and \eqn{1}
#'
#' @param spec
#' number of cores\strong{:}
#' positive integer
#'
#' @details
#' Automatic adjustment of the number of permutations
#' such that Bonferroni-significant p-values are possible.
...
...
@@ -844,7 +848,7 @@ test.single <- function(Y,X,map,i,limit=NULL,steps=NULL,rho=c(0,0.5,1)){
#' @examples
#' NA
#'
test.multiple
<-
function
(
Y
,
X
,
map
,
rho
=
c
(
0
,
0.5
,
1
)){
test.multiple
<-
function
(
Y
,
X
,
map
,
rho
=
c
(
0
,
0.5
,
1
)
,
spec
=
4
){
p
<-
nrow
(
map
$
genes
)
...
...
@@ -871,7 +875,7 @@ test.multiple <- function(Y,X,map,rho=c(0,0.5,1)){
# parallel computation
type
<-
ifelse
(
test
=
.Platform
$
OS.type
==
"windows"
,
yes
=
"PSOCK"
,
no
=
"FORK"
)
cluster
<-
parallel
::
makeCluster
(
spec
=
8
,
type
=
type
)
cluster
<-
parallel
::
makeCluster
(
spec
=
spec
,
type
=
type
)
parallel
::
clusterSetRNGStream
(
cl
=
cluster
,
iseed
=
1
)
parallel
::
clusterExport
(
cl
=
cluster
,
varlist
=
c
(
"Y"
,
"X"
,
"map"
,
"limit"
,
"steps"
,
"rho"
),
envir
=
environment
())
start
<-
Sys.time
()
...
...
docs/reference/test.multiple.html
View file @
81c97798
...
...
@@ -120,7 +120,7 @@
</div>
<pre
class=
"usage"
><span
class=
'fu'
>
test.multiple
</span>
(
<span
class=
'no'
>
Y
</span>
,
<span
class=
'no'
>
X
</span>
,
<span
class=
'no'
>
map
</span>
,
<span
class=
'kw'
>
rho
</span>
<span
class=
'kw'
>
=
</span>
<span
class=
'fu'
>
c
</span>
(
<span
class=
'fl'
>
0
</span>
,
<span
class=
'fl'
>
0.5
</span>
,
<span
class=
'fl'
>
1
</span>
))
</pre>
<pre
class=
"usage"
><span
class=
'fu'
>
test.multiple
</span>
(
<span
class=
'no'
>
Y
</span>
,
<span
class=
'no'
>
X
</span>
,
<span
class=
'no'
>
map
</span>
,
<span
class=
'kw'
>
rho
</span>
<span
class=
'kw'
>
=
</span>
<span
class=
'fu'
>
c
</span>
(
<span
class=
'fl'
>
0
</span>
,
<span
class=
'fl'
>
0.5
</span>
,
<span
class=
'fl'
>
1
</span>
)
,
<span
class=
'kw'
>
spec
</span>
<span
class=
'kw'
>
=
</span>
<span
class=
'fl'
>
4
</span>
)
</pre>
<h2
class=
"hasAnchor"
id=
"arguments"
><a
class=
"anchor"
href=
"#arguments"
></a>
Arguments
</h2>
<table
class=
"ref-arguments"
>
...
...
@@ -144,6 +144,11 @@ matrix with \(n\) rows (samples) and \(q\) columns (SNPs)</p></td>
<th>
rho
</th>
<td><p>
correlation
<strong>
:
</strong>
numeric vector with values between \(0\) and \(1\)
</p></td>
</tr>
<tr>
<th>
spec
</th>
<td><p>
number of cores
<strong>
:
</strong>
positive integer
</p></td>
</tr>
</table>
...
...
man/test.multiple.Rd
View file @
81c97798
...
...
@@ -4,7 +4,7 @@
\alias{test.multiple}
\title{Conduct multiple tests}
\usage{
test.multiple(Y, X, map, rho = c(0, 0.5, 1))
test.multiple(Y, X, map, rho = c(0, 0.5, 1)
, spec = 4
)
}
\arguments{
\item{Y}{exon expression\strong{:}
...
...
@@ -18,6 +18,9 @@ matrix with \eqn{n} rows (samples) and \eqn{q} columns (SNPs)}
\item{rho}{correlation\strong{:}
numeric vector with values between \eqn{0} and \eqn{1}}
\item{spec}{number of cores\strong{:}
positive integer}
}
\description{
This function ...
...
...
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