aggregateRanges: Aggregate GRanges with columns of attached values to genes

In annikabuerger/Cogito: Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets

Aggregate GRanges with columns of attached values to genes

Description

Aggregates multiple GRanges objects with present columns of attached values (mcols) to genes or ranges of given reference of given organism.

Usage

    aggregateRanges(ranges, configfile = NULL, organism = NULL,
                    referenceRanges = NULL, name = "", verbose = FALSE)

Arguments

ranges	list of GRanges, GRangesList or CompressedGRangesList with names in "RRBS|DNA|CNV|RNA|CHiP"
configfile	character, path to configuration file in json format
organism	TxDb or OrganismDb object, default value NULL
referenceRanges	list of GRanges, GRangesList or CompressedGRangesList with length one and name of reference, default value NULL
name	character, default value ""
verbose	logical, default value FALSE

Value

List object with three members: One GRanges object with one gene or range of given reference per line and one column per sample, configuration information, and name.

Author(s)

Annika Bürger

See Also

summarizeRanges

Examples

mm9 <- TxDb.Mmusculus.UCSC.mm9.knownGene::TxDb.Mmusculus.UCSC.mm9.knownGene

### small artificial example ###
ranges.RNA.control <-
    GRanges(seq = "chr10",
            IRanges(c(41023369, 41211825, 41528287, 41994926, 42301673,
                        43256520, 43618919, 49503584, 51349066, 52099001),
                    c(41023544, 41212385, 41528663, 41995357, 42302290,
                        43257075, 43619492, 49504033, 51349425, 52099521)),
            seqinfo = GenomeInfoDb::seqinfo(mm9),
            expr = runif(5, 0, 1))
ranges.RNA.condition <-
    GRanges(seq = "chr10",
            IRanges(c(41013942, 41208731, 41535166, 41999999, 42292275, 
                        43256194, 43615562, 49497888, 51347046, 52092180),
                    c(41014274, 41209664, 41536039, 42000182, 42292965, 
                        43256430, 43615866, 49498362, 51347969, 52092733)),
            seqinfo = GenomeInfoDb::seqinfo(mm9),
            expr = runif(5, 0, 1))
ranges.ChIP.control <-
    GRanges(seq = "chr10",
            IRanges(c(41022835, 41307587, 42197924, 42302387, 42893825,
                        43259749, 43620352, 43721891, 44248812, 45207572,
                        49508713, 51309978, 51348779, 52101900, 52265513),
                    c(41022954, 41307745, 42198201, 42302555, 42893974,
                        43259889, 43620604, 43722051, 44248920, 45207704,
                        49508859, 51310187, 51348921, 52102030, 52265689)),
            seqinfo = GenomeInfoDb::seqinfo(mm9),
            score = round(runif(15, 5, 90)))

example.dataset <- list(RNA = GRangesList(control = ranges.RNA.control, 
                                            condition = ranges.RNA.condition), 
                        ChIP = ranges.ChIP.control)

aggregated.ranges <- aggregateRanges(ranges = example.dataset,
                                        organism = mm9, 
                                        name = "art.example", 
                                        verbose = TRUE)

names(aggregated.ranges)
head(aggregated.ranges$genes)

annikabuerger/Cogito documentation built on July 7, 2022, 4:38 p.m.