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Aurelien Brionne
GenomeFeatures
Commits
ba4a144c
Commit
ba4a144c
authored
Dec 21, 2018
by
Aurelien Brionne
Browse files
gen_table update
parent
ba32286b
Changes
2
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R/build_genome_features.R
View file @
ba4a144c
...
...
@@ -388,7 +388,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
}
###################
# load annotation
sup
plement
# load annotation
com
plement
###################
###################
...
...
@@ -434,7 +434,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
###################
# select columns from gtf
gene_table
<-
gene_table
[,
.
(
seqnames
,
start
,
end
,
strand
,
type
,
gene_
id
,
gene_name
,
gene_biotyp
e
,
transcript_id
)
.
(
seqnames
,
start
,
end
,
strand
,
type
,
gene_
nam
e
,
transcript_id
,
gene_id
)
]
}
else
{
...
...
@@ -448,12 +448,14 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
###################
# extract gene_id
gene_table
[,
`:=`
(
gene_id
=
base
::
sub
(
"^.+:"
,
""
,
Dbxref
[[
1
]][
1
]),
Dbxref
=
NULL
),
gene_id
:=
base
::
sub
(
"^.+:"
,
""
,
Dbxref
[[
1
]][
1
]),
by
=
1
:
base
::
nrow
(
gene_table
)
]
][,
Dbxref
:=
NULL
]
###################
# reneme gene to gene_name
base
::
names
(
gene_table
)[
6
]
<-
"gene_name"
}
}
else
{
...
...
vignettes/introduction.Rmd
View file @
ba4a144c
...
...
@@ -94,6 +94,34 @@ toplevel=GenomicFeatures::makeTxDbFromGFF(
taxonomyId=9031,
dbxrefTag="ID"
)
toplevel=GenomicFeatures::makeTxDbFromGFF(
file=file,
format="gff",
organism="Gallus gallus",
taxonomyId=9031,
dbxrefTag="ID"
)
file="/home/abrionne/Documents/SAVE_uraanabioinfo/programmes_R/GenomeFeatures/inst/extdata/data/input/galGal5.gff"
```
Now, we build a convenient object with `GenomeFeatures::build_genome_features`, needed for find overlaps beetween all selected features and genomic coordinates targets into a single step (see below).
...
...
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