Description Usage Arguments Value Examples
doMatch
computes the number of reads (counts) fall into specific
genomic region such as promoter or genebody for ChIP-Seq, and calculate the
gene expression in counts, and then match the RNA-Seq and ChIP-Seq data on
the gene level with the method of "weighetd mean" or "highest".
1 2 3 4 5 6 7 8 9 10 | doMatch(
rnaMeta,
chipMeta,
region,
method,
ensemblDataset,
host,
fragLength = 180,
promoter.length = 5000
)
|
rnaMeta |
metadata for RNA-Seq include column named "condition" indicates the experiment condition or cell type, and column named "files" indicates the paths of cprresponing abundance.tsv file that is returned from Kallisto. |
chipMeta |
metadata for ChIP-Seq include column of "mark" column indicates the markers of histone modifications, column of "condition" indicates the experiment condition or cell type, and "files" column indicates the paths and the file names of the aligned bam files. |
region |
region has to be specified as "promoter" or "genebody". |
method |
method has to be specified as "weighted.mean" or"highest" if region is set as "promoter". |
ensemblDataset |
Ensembl Dataset you want to use. To see the different datasets available within a biomaRt you can e.g. do: mart = useMart('ensembl'), followed by listDatasets(mart). |
host |
specify the archived versions of Ensembl. To see the available archived versions do: biomaRt::listEnsemblArchives() |
fragLength |
extend reads toward the 3'-end to the average DNA fragment size obtained after DNA size selection. |
promoter.length |
the length of the promoter region. |
A list with the following three items.
res.rna a data frame contains RNA-Seq counts
res.chip a data frame contains ChIP-Seq counts
matched.data a dataframe contains matched RNA-Seq counts and ChIP-Seq counts.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | data(test_rna_meta)
data(test_chip_meta)
for(i in test_rna_meta$SRR){
test_rna_meta$files <- system.file("extdata",paste0(i,".tsv"),
package = "intePareto")
}
for(i in test_chip_meta$SRR){
test_chip_meta$files <- system.file("extdata", paste0(i,".bam"),
package = "intePareto")
}
doMatch(rnaMeta = test_rna_meta,
chipMeta = test_chip_meta,
region = "promoter",
method = "weighted.mean",
host = "http://aug2017.archive.ensembl.org",
ensemblDataset = "mmusculus_gene_ensembl")
|
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