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small tweak to nova-hits example.

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1 parent 77d6ed7 commit 13be90e9f9b3f439cfa58355ba7c354eac4f384d @lianos committed Mar 1, 2012
Showing with 15 additions and 14 deletions.
  1. +15 −14 inst/demos/predict-NOVA-HITS.R
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29 inst/demos/predict-NOVA-HITS.R
@@ -152,6 +152,7 @@ y <- c(rep(1, length(icansplice.dna)), rep(-1, length(neg.dna)))
## C.neg and C are swapped in shikken now (bug) -- wil fix!
## This training take a long time
m <- SVM(X, y, kernel="spectrum", degree=4, C.neg=100000, C=10, threads=2)
+
## Some sequences have N -- this is illegal, The index of these
## sequences have been returned to m
@@ -265,7 +266,7 @@ no.dex <- no.dex[countOverlaps(no.dex, dex.gr) == 0]
# if (FALSE) {
# ag.mm9 <- readRDS('~/cBio/projects/TagSeq/inst/extdata/annotated.genome.mm9.rds')
# ag.dm3 <- readRDS('/Users/stavros/cBio/projects/GenomicCache/GenomicCache.dm3.ensGene/cache/annotated.chromosomes/annotated.collapse-cover.up-500.down-5000.cds-cover-max.rds')
-#
+#
# ## dm3 is duplicated!
# if (FALSE) {
# dt <- as(ag.dm3, 'data.table')
@@ -274,49 +275,49 @@ no.dex <- no.dex[countOverlaps(no.dex, dex.gr) == 0]
# ag.dm3 <- as(u, 'GRanges')
# saveRDS(ag.dm3, '/Users/stavros/cBio/projects/GenomicCache/GenomicCache.dm3.ensGene/cache/annotated.chromosomes/annotated.collapse-cover.up-500.down-5000.cds-cover-max.rds')
# }
-#
+#
# ## dm.exons
# ## load('/Users/stavros/cBio/bioc/BiocSeqSVM/data/Dmel.DEXSeq.exons.rda')
-#
+#
# ## nova.peaks
# load('/Users/stavros/cBio/bioc/BiocSeqSVM/data/NOVA.mm9.rda')
-#
+#
# ## p.counts, dm.exons
# load('/Users/stavros/cBio/bioc/BiocSeqSVM/data/pasillaData.rda')
-#
+#
# dex <- read.table('/Users/stavros/cBio/bioc/BiocSeqSVM/data/ps.diff-exons-some.txt',
# stringsAsFactors=FALSE, header=TRUE, sep="\t")
-#
-#
+#
+#
# library(GenomicCache)
# library(SeqTools)
# gcm <- GenomicCache("/Users/stavros/cBio/projects/GenomicCache/GenomicCache.mm9.knownGene")
# gcd <- GenomicCache('/Users/stavros/cBio/projects/GenomicCache/GenomicCache.dm3.ensGene')
# n1 <- GFGene("Nova1", gcm)
# n2 <- GFGene("Nova2", gcm)
-#
+#
# dl('seqstore')
-#
+#
# bams <- c(wt1='/Users/stavros/cBio/bioc/data/pasilla/untreated-1/tophat_out/accepted_hits.bam',
# wt2='/Users/stavros/cBio/bioc/data/pasilla/untreated-4/tophat_out/accepted_hits.bam',
# ps1='/Users/stavros/cBio/bioc/data/pasilla/ps-si-1/tophat_out/accepted_hits.bam')
# bams <- as.list(bams)
# bams <- lapply(bams, BamFile)
-#
+#
# ## Fly
# ## http://www-huber.embl.de/pub/DEXSeq/psfb/testForDEU.html
# tenm <- GFGene("Ten-m", gcd) ## exon 7: ~ 22362702
# tranges <- ag.mm9[values(ag.mm9)$symbol == "Ten-m"]
# br <- GFGene("br", gcd) ## exon 12 1537033 chrX [1531317, 1531367]
# }
-#
+#
# ################################################################################
# ## AMI setup
# if (FALSE) {
# # ag.mm9 <- readRDS('/home/steve/ml-data/annotated.genome.mm9.rds')
# # ## ag.dm3 <- readRDS('/home/steve/ml-data/annotated.genome.dm3.rds')
# # base <- 'http://cbio.mskcc.org/~lianos/files/bioc2012'
-# #
+# #
# # fetch <- c('Dmel.DEXSeq.exons.rda',
# # 'NOVA.mm9.rda', ## nova.peaks
# # 'pasillaData.rda', ## dm.exons
@@ -328,7 +329,7 @@ no.dex <- no.dex[countOverlaps(no.dex, dex.gr) == 0]
# # }
# # }
# # ag.dm3 <- readRDS('dm3.anno.rds')
-# #
+# #
# # dex <- system.file("data", "ps.diff-exons.txt", package="BiocSeqSVM")
# }
-#
+#

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