BED2RangedData {ChIPpeakAnno} | R Documentation

## Convert BED format to RangedData

### Description

Convert BED format to RangedData. This function will be depreciated.

### Usage

    BED2RangedData(data.BED,header=FALSE, ...)

### Arguments

`data.BED` | BED format data frame or BED filename, please refer to http://genome.ucsc.edu/FAQ/FAQformat#format1 for details
`header` | TRUE or FALSE, default to FALSE, indicates whether data.BED file has BED header
`...` | any parameter need to be passed into read.delim function

### Value

RangedData with slot start holding the start position of the feature, slot end holding the end position of the feature, slot names holding the id of the feature, slot space holding the chromosome location where the feature is located. In addition, the following variables are included.

``strand`` | 1 for positive strand and -1 for negative strand where the feature is located. Default to 1 if not present in the BED formated data frame

### Note

For converting the peakList in BED format to RangedData before calling annotatePeakInBatch function

### Author(s)

Lihua Julie Zhu

### See Also

See also as `toGRanges`.

### Examples

        test.bed = data.frame(cbind(chrom = c("1", "2"),
                              chromStart=c("100", "1000"),
                              chromEnd=c("200", "1100"),
                              name=c("peak1", "peak2")))
        test.rangedData = BED2RangedData(test.bed)

[Package ChIPpeakAnno version 3.12.7 Index]