Nothing
### =========================================================================
### Timing findOverlaps() and summarizeOverlaps()
### -------------------------------------------------------------------------
library(RNAseqData.HNRNPC.bam.chr14)
bamfile <- RNAseqData.HNRNPC.bam.chr14_BAMFILES[1]
library(GenomicAlignments)
reads <- readGAlignments(bamfile)
reads_grl <- grglist(reads)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
exbygene <- exonsBy(txdb, by="gene")
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Timing findOverlaps,GRangesList,GRangesList method
###
system.time(hits1 <- findOverlaps(exbygene, reads_grl))
#digest(hits1) # "42f770fcf1a2f27f2ceeb18249244677"
# With BioC 3.0 / R 3.1
# ---------------------
# First time:
# user system elapsed
# 1.999 0.020 2.022
# Subsequent times:
# user system elapsed
# 0.852 0.000 0.854
# With BioC 3.1/ R 3.2
# --------------------
# First time:
# user system elapsed
# 0.797 0.008 0.806
# Subsequent times:
# user system elapsed
# 0.141 0.000 0.141
system.time(hits2 <- findOverlaps(exbygene, reads_grl, ignore.strand=TRUE))
#digest(hits2) # "3f1a62b338d431ef2705602ce6dfbf9a"
# With BioC 3.0 / R 3.1
# ---------------------
# First time:
# user system elapsed
# 3.605 0.020 3.629
# Subsequent times:
# user system elapsed
# 1.152 0.000 1.154
# With BioC 3.1/ R 3.2
# --------------------
# First time:
# user system elapsed
# 1.244 0.008 1.254
# Subsequent times:
# user system elapsed
# 0.170 0.000 0.171
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Timing findOverlaps,GRangesList,GAlignments method
###
system.time(hits3 <- findOverlaps(exbygene, reads))
#digest(hits3) # "42f770fcf1a2f27f2ceeb18249244677"
# With BioC 3.0 / R 3.1
# ---------------------
# First time:
# user system elapsed
# 3.844 0.016 3.864
# Subsequent times:
# user system elapsed
# 1.093 0.000 1.095
# With BioC 3.1/ R 3.2
# --------------------
# First time:
# user system elapsed
# 1.792 0.008 1.802
# Subsequent times:
# user system elapsed
# 0.366 0.000 0.367
system.time(hits4 <- findOverlaps(exbygene, reads, ignore.strand=TRUE))
#digest(hits4) # "3f1a62b338d431ef2705602ce6dfbf9a"
# With BioC 3.0 / R 3.1
# ---------------------
# First time:
# user system elapsed
# 5.075 0.004 5.084
# Subsequent times:
# user system elapsed
# 2.642 0.012 2.658
# With BioC 3.1/ R 3.2
# --------------------
# First time:
# user system elapsed
# 1.766 0.004 1.771
# Subsequent times:
# user system elapsed
# 0.396 0.000 0.397
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Timing summarizeOverlaps,GRangesList,GAlignments method
###
system.time(se1 <- summarizeOverlaps(exbygene, reads))
#digest(assay(se1)) # "7e58dc4eb0c56fbf75ff86c09dbafb90"
# With BioC 3.0 / R 3.1
# ---------------------
# First time:
# user system elapsed
# 3.815 0.012 3.831
# Subsequent times:
# user system elapsed
# 1.361 0.000 1.363
# With BioC 3.1/ R 3.2
# --------------------
# First time:
# user system elapsed
# 1.783 0.004 1.789
# Subsequent times:
# user system elapsed
# 0.436 0.004 0.441
system.time(se2 <- summarizeOverlaps(exbygene, reads, ignore.strand=TRUE))
#digest(assay(se2)) # "7d473582932ee5704acbddd1ffc5c146"
# With BioC 3.0 / R 3.1
# ---------------------
# First time:
# user system elapsed
# 5.545 0.020 5.570
# Subsequent times:
# user system elapsed
# 2.614 0.000 2.617
# With BioC 3.1/ R 3.2
# --------------------
# First time:
# user system elapsed
# 2.489 0.004 2.495
# Subsequent times:
# user system elapsed
# 0.490 0.008 0.498
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