aggregateRanges {Cogito} | R Documentation

## Aggregate GRanges with columns of attached values to genes

### Description

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

### Usage

        aggregateRanges(ranges, configfile = NULL, organism = 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
`name` | character, default value ""
`verbose` | logical, default value FALSE

### Value

List object with three members: One GRanges object with one gene 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)

[Package Cogito version 1.0.0 Index]