differential.coverage: differential.coverage: is a collection of routines useful for...
In favorov/differential.coverage: Differential Coverage package
Description
Preparing probes
Test differential intersection of the prbes with a set of intervals
Annotation functions
Description
differential.coverage is more or less random collection of procedures that are useful for differential analysis of interval sets.
Each set represents a genomwide experiment (probably, MBD, but actually, we just suppose it to be an interval genomewide coverage).
The package provides three classes of functions: prepare probes, test differntial intersection of probes with a collection of intervals, and annotation.
Preparing probes
The probes is a set of genomic intervels. It actually can be some pre-given set of genomic intervals (e.g. open chromatin intervals or CpG islands), but if we want to be agnostic, we can prepare a
uniform tiling of all the genome. We also can 'inflate' all the probes (intervals).
prepare.covering.noodles
inflate.noodles
Test differential intersection of the prbes with a set of intervals
The probes we have is a common gemtry for all the samples we work with. Also, for each sample, we have set of genomic intervals (lets' call the peaks), e.g. MACS results for a MBDseq,
and the samples belong to (two) conditions and for each probe we want to test null hypethesis that the probe interval is equally prone to be intersected with the peaks.
count.coverage.of.noodles
indicate.any.coverage.of.noodles
max.peak.score.for.each.noodle
prepare.tabulated.fisher
tab.fisher.row.no
Annotation functions
After we run the tests and filter the probes to have the differentialy covered oned, or for any other interval annotation, we can run the annotation functions to idetify the genes around.
The package knows the gene annotatinos of the following genomes: ucsc mm9 and mm10, gencode mm23, mm24 and mm25, ucsc hg 18, hg19, hg38, and gencode hs19, hs26, hs28, hs29, hs32 and hs34.
The functions are:
closest.gene.by.interval
closest.gene.start.by.interval
genes.intersected
genes.intersected.by.interval
genes.with.TSS.covered
genes.with.TSS.covered.by.interval
get.Known.Gene.List
preceded.gene.by.interval
favorov/differential.coverage documentation built on Feb. 18, 2022, 5:50 p.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Preparing probes Test differential intersection of the prbes with a set of intervals Annotation functions
Description
differential.coverage is more or less random collection of procedures that are useful for differential analysis of interval sets.
Each set represents a genomwide experiment (probably, MBD, but actually, we just suppose it to be an interval genomewide coverage).
The package provides three classes of functions: prepare probes, test differntial intersection of probes with a collection of intervals, and annotation.
Preparing probes
The probes is a set of genomic intervels. It actually can be some pre-given set of genomic intervals (e.g. open chromatin intervals or CpG islands), but if we want to be agnostic, we can prepare a
uniform tiling of all the genome. We also can 'inflate' all the probes (intervals).
prepare.covering.noodles
inflate.noodles
Test differential intersection of the prbes with a set of intervals
The probes we have is a common gemtry for all the samples we work with. Also, for each sample, we have set of genomic intervals (lets' call the peaks), e.g. MACS results for a MBDseq,
and the samples belong to (two) conditions and for each probe we want to test null hypethesis that the probe interval is equally prone to be intersected with the peaks.
count.coverage.of.noodles
indicate.any.coverage.of.noodles
max.peak.score.for.each.noodle
prepare.tabulated.fisher
tab.fisher.row.no
Annotation functions
After we run the tests and filter the probes to have the differentialy covered oned, or for any other interval annotation, we can run the annotation functions to idetify the genes around.
The package knows the gene annotatinos of the following genomes: ucsc mm9 and mm10, gencode mm23, mm24 and mm25, ucsc hg 18, hg19, hg38, and gencode hs19, hs26, hs28, hs29, hs32 and hs34.
The functions are:
closest.gene.by.interval
closest.gene.start.by.interval
genes.intersected
genes.intersected.by.interval
genes.with.TSS.covered
genes.with.TSS.covered.by.interval
get.Known.Gene.List
preceded.gene.by.interval
R Package Documentation
Browse R Packages
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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