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bioinfo
datautils
Commits
9b213795
Commit
9b213795
authored
Apr 27, 2017
by
Holger Brandl
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use remote kegg for enrichment (since local data is buggy and comes without IDs)
parent
4f57eeb8
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R/bio/cp_utils.R
R/bio/cp_utils.R
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R/bio/cp_utils.R
View file @
9b213795
...
...
@@ -64,6 +64,7 @@ find_enr_terms = function(ensemblIds, ...){
cp_test
=
function
(
geneIds
,
annoDb
,
cp_species
,
q_cutoff
=
0.05
){
# DEBUG geneIds <- glMapped %>% filter(cluster %in% c("cluster_9")) %$% entrez_gene_id %>% as.integer
# DEBUG geneIds <- glMapped %>% filter(cluster_id %in% c("nr1")) %$% entrez_gene_id %>% as.integer
# DEBUG geneIds <- head(glMapped,30)$entrez_gene_id
# geneIds=.$entrez_gene_id
...
...
@@ -76,7 +77,7 @@ cp_test = function(geneIds, annoDb, cp_species, q_cutoff=0.05){
# PANTHER10_ontology <- read.delim("http://data.pantherdb.org/PANTHER10.0/ontology/Protein_Class_7.0")
# pantherResults <- enricher(gene = geneIds, organism = cp_species, qvalueCutoff = q_cutoff, readable = TRUE, TERM2GENE = PANTHER10_ontology) %>% summary()
keggResults
<-
clusterProfiler
::
enrichKEGG
(
gene
=
geneIds
,
organism
=
cp_species
,
qvalueCutoff
=
q_cutoff
,
use_internal_data
=
T
)
%>%
as.data.frame
()
keggResults
<-
clusterProfiler
::
enrichKEGG
(
gene
=
geneIds
,
organism
=
cp_species
,
qvalueCutoff
=
q_cutoff
)
%>%
as.data.frame
()
reactomeResults
<-
ReactomePA
::
enrichPathway
(
gene
=
geneIds
,
organism
=
cp_species
,
qvalueCutoff
=
q_cutoff
)
%>%
as.data.frame
()
goResultsCC
<-
clusterProfiler
::
enrichGO
(
gene
=
geneIds
,
OrgDb
=
annoDb
,
qvalueCutoff
=
q_cutoff
,
ont
=
"CC"
)
%>%
as.data.frame
()
goResultsMF
<-
clusterProfiler
::
enrichGO
(
gene
=
geneIds
,
OrgDb
=
annoDb
,
qvalueCutoff
=
q_cutoff
,
ont
=
"MF"
)
%>%
as.data.frame
()
...
...
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