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Armin Rauschenberger
joinet
Commits
db8d7591
Commit
db8d7591
authored
Jun 27, 2018
by
Rauschenberger
Browse files
automation
parent
89c44907
Changes
6
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Inline
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R/functions.R
View file @
db8d7591
...
...
@@ -81,7 +81,8 @@ get.snps.geuvadis <- function(chr,path=getwd()){
#' data directory
#'
#' @param size
#' maximum number of SNPs to read in at once
#' maximum number of SNPs to read in at once;
#' trade-off between memory usage (low) and speed (high)
#'
#' @examples
#' path <- "/virdir/Scratch/arauschenberger/trial"
...
...
@@ -92,7 +93,6 @@ get.snps.bbmri <- function(chr,biobank=NULL,path=getwd(),size=500*10^3){
message
(
rep
(
"-"
,
times
=
20
),
" chromosome "
,
chr
,
" "
,
rep
(
"-"
,
times
=
20
))
p
<-
5
*
10
^
6
# (maximum number of SNPs per chromosome, before filtering)
# size <- 60*10^3 # (originally 100*10^3, decrease: slower but less memory)
skip
<-
seq
(
from
=
0
,
to
=
p
,
by
=
size
)
if
(
is.null
(
biobank
)){
study
<-
c
(
"CODAM"
,
"LL"
,
"LLS0"
,
"LLS1"
,
"NTR0"
,
"NTR1"
,
"PAN"
,
"RS"
)
...
...
@@ -120,7 +120,7 @@ get.snps.bbmri <- function(chr,biobank=NULL,path=getwd(),size=500*10^3){
if
(
study
[
j
]
==
"NTR0"
){
dir
<-
"NTR/Affy6"
}
if
(
study
[
j
]
==
"NTR1"
){
dir
<-
"NTR/GoNL"
}
path0
<-
file.path
(
"/mnt/virdir/Backup/RP3_data/HRCv1.1_Imputation"
,
dir
)
path1
<-
"/virdir/Scratch/arauschenberger/trial"
path1
<-
path
file0
<-
paste0
(
"chr"
,
chr
,
".dose.vcf.gz"
)
file1
<-
paste0
(
study
[
j
],
".chr"
,
chr
,
".dose.vcf.gz"
)
file2
<-
paste0
(
study
[
j
],
".chr"
,
chr
,
".dose.vcf"
)
...
...
@@ -169,7 +169,7 @@ get.snps.bbmri <- function(chr,biobank=NULL,path=getwd(),size=500*10^3){
# Removing empty rows.
cond
<-
apply
(
collect
,
1
,
function
(
x
)
all
(
sapply
(
x
,
length
)
==
0
))
collect
<-
collect
[
!
cond
,,
drop
=
FALSE
]
save
(
object
=
collect
,
file
=
file.path
(
path1
,
paste0
(
"temp.chr"
,
chr
,
".RData"
)))
#
save(object=collect,file=file.path(path1,paste0("temp.chr",chr,".RData")))
#load(file.path(path1,paste0("temp.chr",chr,".RData")))
# Fusing all matrices.
...
...
@@ -190,19 +190,20 @@ get.snps.bbmri <- function(chr,biobank=NULL,path=getwd(),size=500*10^3){
# Filter samples.
rownames
(
snps
)
<-
sub
(
x
=
rownames
(
snps
),
pattern
=
"LLS0|LLS1"
,
replacement
=
"LLS"
)
rownames
(
snps
)
<-
sub
(
x
=
rownames
(
snps
),
pattern
=
"NTR0|NTR1"
,
replacement
=
"NTR"
)
#split <- strsplit(x=colnames(snps),split=":")
#bio <- sapply(split,function(x) x[[1]])
#id <- sapply(split,function(x) x[[2]])
#cond <- rep(NA,times=ncol(snps))
#for(j in seq_along(study)){
# cond[bio==study[j]] <- duplicated(id[bio==study[j]])
#}
if
(
is.null
(
biobank
)){
save
(
object
=
snps
,
file
=
file.path
(
path1
,
paste0
(
"BBMRI.chr"
,
chr
,
".RData"
)))
}
else
{
save
(
object
=
snps
,
file
=
file.path
(
path1
,
paste0
(
biobank
,
".chr"
,
chr
,
".RData"
)))
}
# Remove temporary files.
for
(
j
in
seq_along
(
study
)){
file1
<-
paste0
(
study
[
j
],
".chr"
,
chr
,
".dose.vcf.gz"
)
file2
<-
paste0
(
study
[
j
],
".chr"
,
chr
,
".dose.vcf"
)
file.remove
(
file.path
(
path1
,
c
(
file1
,
file2
)))
}
}
...
...
@@ -605,7 +606,7 @@ map.snps <- function(gene.chr,gene.start,gene.end,snp.chr,snp.pos,dist=10^3){
#' @export
#' @title
#' Drop trivial test
#' Drop trivial test
s
#'
#' @description
#' This function
...
...
docs/reference/drop.trivial.html
View file @
db8d7591
...
...
@@ -6,7 +6,7 @@
<meta
http-equiv=
"X-UA-Compatible"
content=
"IE=edge"
>
<meta
name=
"viewport"
content=
"width=device-width, initial-scale=1.0"
>
<title>
Drop trivial test — drop.trivial • spliceQTL
</title>
<title>
Drop trivial test
s
— drop.trivial • spliceQTL
</title>
<!-- jquery -->
<script
src=
"https://code.jquery.com/jquery-3.1.0.min.js"
integrity=
"sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
crossorigin=
"anonymous"
></script>
...
...
@@ -28,7 +28,7 @@
<meta
property=
"og:title"
content=
"Drop trivial test — drop.trivial"
/>
<meta
property=
"og:title"
content=
"Drop trivial test
s
— drop.trivial"
/>
<meta
property=
"og:description"
content=
"This function"
/>
<meta
name=
"twitter:card"
content=
"summary"
/>
...
...
@@ -109,7 +109,7 @@
<div
class=
"row"
>
<div
class=
"col-md-9 contents"
>
<div
class=
"page-header"
>
<h1>
Drop trivial test
</h1>
<h1>
Drop trivial test
s
</h1>
<small
class=
"dont-index"
>
Source:
<a
href=
'https://github.com/rauschenberger/spliceQTL/blob/master/R/functions.R'
><code>
R/functions.R
</code></a></small>
<div
class=
"hidden name"
><code>
drop.trivial.Rd
</code></div>
</div>
...
...
docs/reference/get.snps.bbmri.html
View file @
db8d7591
...
...
@@ -139,7 +139,8 @@
</tr>
<tr>
<th>
size
</th>
<td><p>
maximum number of SNPs to read in at once
</p></td>
<td><p>
maximum number of SNPs to read in at once;
trade-off between memory usage (low) and speed (high)
</p></td>
</tr>
</table>
...
...
docs/reference/index.html
View file @
db8d7591
...
...
@@ -176,7 +176,7 @@
<td>
<p><code><a
href=
"drop.trivial.html"
>
drop.trivial()
</a></code>
</p>
</td>
<td><p>
Drop trivial test
</p></td>
<td><p>
Drop trivial test
s
</p></td>
</tr><tr>
<!-- -->
<td>
...
...
man/drop.trivial.Rd
View file @
db8d7591
...
...
@@ -2,7 +2,7 @@
% Please edit documentation in R/functions.R
\name{drop.trivial}
\alias{drop.trivial}
\title{Drop trivial test}
\title{Drop trivial test
s
}
\usage{
drop.trivial(map)
}
...
...
man/get.snps.bbmri.Rd
View file @
db8d7591
...
...
@@ -13,7 +13,8 @@ get.snps.bbmri(chr, biobank = NULL, path = getwd(), size = 500 * 10^3)
\item{path}{data directory}
\item{size}{maximum number of SNPs to read in at once}
\item{size}{maximum number of SNPs to read in at once;
trade-off between memory usage (low) and speed (high)}
}
\description{
This function transforms SNP data (virtual machine).
...
...
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