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Armin Rauschenberger
joinet
Commits
49360ff7
Commit
49360ff7
authored
Aug 21, 2018
by
Rauschenberger
Browse files
automation
parent
bd61088d
Changes
4
Show whitespace changes
Inline
Side-by-side
R/functions.R
View file @
49360ff7
...
...
@@ -536,7 +536,7 @@ adjust.variables <- function(x,offset,group){
map.genes
<-
function
(
chr
,
path
=
getwd
(),
release
=
"GRCh37"
,
build
=
71
){
# check input
if
(
!
chr
%in%
1
:
22
){
if
((
!
is.null
(
chr
))
&&
(
!
chr
%in%
1
:
22
)
)
{
stop
(
"Invalid argument \"chr\"."
,
call.
=
FALSE
)
}
if
(
!
release
%in%
c
(
"NCBI36"
,
"GRCh37"
,
"GRCh38"
)){
...
...
@@ -558,8 +558,12 @@ map.genes <- function(chr,path=getwd(),release="GRCh37",build=71){
refGenome
::
basedir
(
object
)
<-
path
refGenome
::
read.gtf
(
object
,
filename
=
file
)
x
<-
refGenome
::
getGenePositions
(
object
=
object
,
by
=
"gene_id"
)
if
(
is.null
(
chr
)){
x
<-
x
[
x
$
gene_biotype
==
"protein_coding"
,]
}
else
{
x
<-
x
[
x
$
seqid
==
chr
&
x
$
gene_biotype
==
"protein_coding"
,]
x
<-
x
[,
c
(
"gene_id"
,
"seqid"
,
"start"
,
"end"
)]
}
x
<-
x
[,
c
(
"gene_id"
,
"seqid"
,
"start"
,
"end"
,
"gene_name"
)]
# added "gene_name"
rownames
(
x
)
<-
NULL
colnames
(
x
)[
colnames
(
x
)
==
"seqid"
]
<-
"chr"
return
(
x
)
...
...
docs/articles/code.html
View file @
49360ff7
...
...
@@ -182,8 +182,8 @@
<a
class=
"sourceLine"
id=
"cb5-8"
data-line-number=
"8"
>
}
</a>
<a
class=
"sourceLine"
id=
"cb5-9"
data-line-number=
"9"
>
}
</a></code></pre></div>
<p>
On the virtual machine, execute this chunk to compare the results between the Geuvadis and the BBMRI project.
</p>
<div
class=
"sourceCode"
id=
"cb6"
><pre
class=
"sourceCode r"
><code
class=
"sourceCode r"
><a
class=
"sourceLine"
id=
"cb6-1"
data-line-number=
"1"
>
list
<
-
<span
class=
"st"
>
</span><span
class=
"kw"
>
list
</span>
(
)
</a>
<a
class=
"sourceLine"
id=
"cb6-2"
data-line-number=
"2"
>
table
<
-
<span
class=
"st"
>
</span><span
class=
"kw"
>
data.frame
</span>
(
<span
class=
"dt"
>
chr=
</span><span
class=
"kw"
>
seq_len
</span>
(
<span
class=
"dv"
>
22
</span>
)
)
</a>
<div
class=
"sourceCode"
id=
"cb6"
><pre
class=
"sourceCode r"
><code
class=
"sourceCode r"
><a
class=
"sourceLine"
id=
"cb6-1"
data-line-number=
"1"
>
table
<
-
<span
class=
"st"
>
</span><span
class=
"kw"
>
data.frame
</span>
(
<span
class=
"dt"
>
chr=
</span><span
class=
"kw"
>
seq_len
</span>
(
<span
class=
"dv"
>
22
</span>
)
)
</a>
<a
class=
"sourceLine"
id=
"cb6-2"
data-line-number=
"2"
>
list
<
-
<span
class=
"st"
>
</span><span
class=
"kw"
>
list
</span>
(
)
</a>
<a
class=
"sourceLine"
id=
"cb6-3"
data-line-number=
"3"
><span
class=
"cf"
>
for
</span>
(i
<span
class=
"cf"
>
in
</span>
<span
class=
"kw"
>
seq_len
</span>
(
<span
class=
"dv"
>
22
</span>
)){
</a>
<a
class=
"sourceLine"
id=
"cb6-4"
data-line-number=
"4"
>
<span
class=
"co"
>
# load p-values
</span></a>
<a
class=
"sourceLine"
id=
"cb6-5"
data-line-number=
"5"
>
<span
class=
"kw"
>
load
</span>
(
<span
class=
"kw"
>
file.path
</span>
(path,
<span
class=
"kw"
>
paste0
</span>
(
<span
class=
"st"
>
"pval.Geuvadis.chr"
</span>
,i,
<span
class=
"st"
>
".RData"
</span>
)))
</a>
...
...
@@ -228,9 +228,12 @@
<a
class=
"sourceLine"
id=
"cb6-44"
data-line-number=
"44"
>
list[[i]]
<
-
<span
class=
"st"
>
</span><span
class=
"kw"
>
data.frame
</span>
(
<span
class=
"dt"
>
chr=
</span>
i,
<span
class=
"dt"
>
gene=
</span><span
class=
"kw"
>
names
</span>
(a),
<span
class=
"dt"
>
Geuvadis=
</span><span
class=
"dv"
>
1
</span><span
class=
"op"
>
*
</span>
a,
<span
class=
"dt"
>
LLS=
</span><span
class=
"dv"
>
1
</span><span
class=
"op"
>
*
</span>
b,
<span
class=
"dt"
>
row.names=
</span><span
class=
"kw"
>
seq_along
</span>
(a))
</a>
<a
class=
"sourceLine"
id=
"cb6-45"
data-line-number=
"45"
>
</a>
<a
class=
"sourceLine"
id=
"cb6-46"
data-line-number=
"46"
>
}
</a>
<a
class=
"sourceLine"
id=
"cb6-47"
data-line-number=
"47"
>
list
<
-
<span
class=
"st"
>
</span><span
class=
"kw"
>
do.call
</span>
(
<span
class=
"dt"
>
what=
</span><span
class=
"st"
>
"rbind"
</span>
,
<span
class=
"dt"
>
args=
</span>
list)
</a>
<a
class=
"sourceLine"
id=
"cb6-48"
data-line-number=
"48"
><span
class=
"kw"
>
save
</span>
(list,
<span
class=
"dt"
>
file=
</span><span
class=
"st"
>
"list.RData"
</span>
)
</a>
<a
class=
"sourceLine"
id=
"cb6-49"
data-line-number=
"49"
><span
class=
"kw"
>
save
</span>
(table,
<span
class=
"dt"
>
file=
</span><span
class=
"st"
>
"table.RData"
</span>
)
</a></code></pre></div>
<a
class=
"sourceLine"
id=
"cb6-47"
data-line-number=
"47"
><span
class=
"kw"
>
save
</span>
(table,
<span
class=
"dt"
>
file=
</span><span
class=
"st"
>
"table.RData"
</span>
)
</a>
<a
class=
"sourceLine"
id=
"cb6-48"
data-line-number=
"48"
></a>
<a
class=
"sourceLine"
id=
"cb6-49"
data-line-number=
"49"
>
list
<
-
<span
class=
"st"
>
</span><span
class=
"kw"
>
do.call
</span>
(
<span
class=
"dt"
>
what=
</span><span
class=
"st"
>
"rbind"
</span>
,
<span
class=
"dt"
>
args=
</span>
list)
</a>
<a
class=
"sourceLine"
id=
"cb6-50"
data-line-number=
"50"
>
names
<
-
<span
class=
"st"
>
</span><span
class=
"kw"
>
do.call
</span>
(
<span
class=
"dt"
>
what=
</span><span
class=
"st"
>
"rbind"
</span>
,
<span
class=
"dt"
>
args=
</span>
list)
</a>
<a
class=
"sourceLine"
id=
"cb6-51"
data-line-number=
"51"
>
list
<span
class=
"op"
>
$
</span>
symbol
<
-
<span
class=
"st"
>
</span>
names
<span
class=
"op"
>
$
</span>
gene_name[
<span
class=
"kw"
>
match
</span>
(
<span
class=
"dt"
>
x=
</span>
list
<span
class=
"op"
>
$
</span>
gene,names
<span
class=
"op"
>
$
</span>
gene_id)]
</a>
<a
class=
"sourceLine"
id=
"cb6-52"
data-line-number=
"52"
><span
class=
"kw"
>
save
</span>
(list,
<span
class=
"dt"
>
file=
</span><span
class=
"st"
>
"list.RData"
</span>
)
</a></code></pre></div>
<p>
On the virtual machine, execute this chunk to plot correlations between SNPs and exons (unclear which genes should be examined).
</p>
<div
class=
"sourceCode"
id=
"cb7"
><pre
class=
"sourceCode r"
><code
class=
"sourceCode r"
><a
class=
"sourceLine"
id=
"cb7-1"
data-line-number=
"1"
>
data
<
-
<span
class=
"st"
>
"LLS"
</span>
<span
class=
"co"
>
# "Geuvadis" or "LLS"
</span></a>
<a
class=
"sourceLine"
id=
"cb7-2"
data-line-number=
"2"
>
chr
<
-
<span
class=
"st"
>
</span><span
class=
"dv"
>
22
</span>
<span
class=
"co"
>
# 1,2,3,...,22
</span></a>
...
...
docs/reference/grid-1.png
View replaced file @
bd61088d
View file @
49360ff7
11.3 KB
|
W:
|
H:
11 KB
|
W:
|
H:
2-up
Swipe
Onion skin
vignettes/code.Rmd
View file @
49360ff7
...
...
@@ -119,8 +119,8 @@ for(chr in 22:1){ # 22:1
On the virtual machine, execute this chunk to compare the results between the Geuvadis and the BBMRI project.
```{r,eval=FALSE}
list <- list()
table <- data.frame(chr=seq_len(22))
list <- list()
for(i in seq_len(22)){
# load p-values
load(file.path(path,paste0("pval.Geuvadis.chr",i,".RData")))
...
...
@@ -165,9 +165,12 @@ for(i in seq_len(22)){
list[[i]] <- data.frame(chr=i,gene=names(a),Geuvadis=1*a,LLS=1*b,row.names=seq_along(a))
}
save(table,file="table.RData")
list <- do.call(what="rbind",args=list)
names <- do.call(what="rbind",args=list)
list$symbol <- names$gene_name[match(x=list$gene,names$gene_id)]
save(list,file="list.RData")
save(table,file="table.RData")
```
On the virtual machine, execute this chunk to plot correlations between SNPs and exons (unclear which genes should be examined).
...
...
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