Mercurial > repos > kpbioteam > minfi_dmr
changeset 19:0fae75cb6146 draft
planemo upload for repository https://github.com/kpbioteam/minfi_dmr commit 65d01f00526cadfcd1f52d06243fbc87ffee462f-dirty
| author | kpbioteam |
|---|---|
| date | Tue, 12 Jun 2018 12:02:18 -0400 |
| parents | 5dba3e018990 |
| children | 3d15f8823c98 |
| files | minfi_dmr.R |
| diffstat | 1 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/minfi_dmr.R Tue Jun 12 11:56:46 2018 -0400 +++ b/minfi_dmr.R Tue Jun 12 12:02:18 2018 -0400 @@ -47,7 +47,8 @@ nullMethod <- input8 coef <- 2 #default verbose <- input9 - +meth <- as.numeric(input10) + dmrs <- bumphunter(GRSet, design = design.matrix, cluster = cluster, @@ -59,6 +60,6 @@ dmrGR <- with(dmrs$table,GRanges(chr,IRanges(start,end),area=area,value=value)) -dmrGR$type <- ifelse(abs(dmrGR$value)<input10, "neither", ifelse(dmrGR$value<0,"hypo","hyper")) +dmrGR$type <- ifelse(abs(dmrGR$value)<meth, "neither", ifelse(dmrGR$value<0,"hypo","hyper")) write.table(dmrGR, file= output1, quote = FALSE, row.names = FALSE, sep = "\t")