addGeneAligns: Reads a bamRange object for a given 'bamReader', 'refGenome'...
In spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
Locates gene in genome via refGenome and reads a
bamRange from the determined region.
Usage
1
Arguments
x
gapSites. The result contains a copy of the passed object.
Details
The function adds a gene_aligns column
to the contained data.frame.
Value
gapSites
Author(s)
Wolfgang Kaisers
Examples
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# A) Read gapSites
bam <- system.file("extdata", "rna_fem.bam", package="spliceSites")
reader <- bamReader(bam, idx=TRUE)
ga <- alignGapList(reader)
bamClose(reader)
# B) Annotate
ucf <- system.file("extdata", "uc_small_junc.RData", package="spliceSites")
ucj <- loadGenome(ucf)
annotation(ga) <- annotate(ga, ucj)
# C) align part
gal <- addGeneAligns(ga)
gal
spliceSites documentation built on May 6, 2019, 3:05 a.m.
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Description Usage Arguments Details Value Author(s) Examples
Description
Locates gene in genome via refGenome and reads a
bamRange from the determined region.
Usage
1 |
Arguments
x |
gapSites. The result contains a copy of the passed object. |
Details
The function adds a gene_aligns column
to the contained data.frame.
Value
gapSites
Author(s)
Wolfgang Kaisers
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | # A) Read gapSites
bam <- system.file("extdata", "rna_fem.bam", package="spliceSites")
reader <- bamReader(bam, idx=TRUE)
ga <- alignGapList(reader)
bamClose(reader)
# B) Annotate
ucf <- system.file("extdata", "uc_small_junc.RData", package="spliceSites")
ucj <- loadGenome(ucf)
annotation(ga) <- annotate(ga, ucj)
# C) align part
gal <- addGeneAligns(ga)
gal
|
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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