library(CIE)
dge <- read.table("/path/to/sample/inputs/sample_input_myc.txt",
header=T, sep="\t")
tissChIP <- filterChIPAtlas(NA, NA, NA, cellLineType="all", tissueCorrect=TRUE,
databaseDir="path/to/tissueCorrectedChIP/")
tissChIP.myc <- runCIE(DGEs=dge,
methods="Ternary",
ents=tissChIP$ChIPall.ents,
rels=tissChIP$ChIPall.rels,
useFile=FALSE)
write.table(tissChIP.myc, "documentation/tissChIPmyc.tsv", quote=F,
sep="\t", row.names=FALSE)
string.myc <- runCIE(DGEs=dge,
methods="Quaternary",
databaseType="string",
databaseDir="path/to/ents/and/rels/files/")
write.table(string.myc, "documentation/stringMyc.tsv", quote=F,
sep="\t", row.names=FALSE)
trrust.myc <- runCIE(DGEs=dge,
methods="Fisher",
databaseType="TRRUST",
databaseDir="path/to/ents/and/rels/files/")
write.table(trrust.myc, "documentation/trrustMYC.tsv", quote=F,
sep="\t", row.names=FALSE)
library(rcytoscapejs)
string <- lapply(c("ents", "rels"), function(x) {
read.table(paste0("path/to/ents/rels/string.", x),
header=T, sep="\t")
})
names(string) <- c("ents", "rels")
trrust <- lapply(c("ents", "rels"), function(x) {
read.table(paste0("path/to/ents/rels/TRRUST.", x),
header=T, sep="\t")
})
names(trrust) <- c("ents", "rels")
createCytoGraph(enrichment=tissChIP.myc, ents=tissChIP$ChIPall.ents,
rels=tissChIP$ChIPall.rels, DGEs=dge)
createCytoGraph(enrichment=string.myc, ents=string$ents,
rels=string$rels, DGEs=dge)
createCytoGraph(enrichment=trrust.myc, ents=trrust$ents,
rels=trrust$rels, DGEs=dge)
pTcMYC <- pathwayEnrichment(tissChIP.myc$name[1:20],)
pStMYC <- pathwayEnrichment(string.myc$name[1:20],)
pTrMYC <- pathwayEnrichment(trrust.myc$name[1:20],)
write.table(pTcMYC, "documentation/pathTcMYC.tsv", quote=F,
sep="\t", row.names=FALSE)
write.table(pStMYC, "documentation/pathStMYC.tsv", quote=F,
sep="\t", row.names=FALSE)
write.table(pTrMYC, "documentation/pathTrMYC.tsv", quote=F,
sep="\t", row.names=FALSE)
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