ranges_for_coords {cicero} | R Documentation

## Construct GRanges objects from coordinate strings

### Description

Construct GRanges objects from coordinate strings

### Usage

    ranges_for_coords(coord_strings, meta_data_df = NULL, with_names = FALSE)

### Arguments

`coord_strings` | A list of coordinate strings (in the form "chr1:500000-1000000")
`meta_data_df` | A data frame with any meta data columns you want included with the ranges. Must be in the same order as coord_strings.
`with_names` | logical - should meta data include coordinate string (field coord_string)?

### Details

Coordinate strings consist of three pieces of information: chromosome, start, and stop. These pieces of information can be separated by the characters ":", "_", or "-". Commas will be removed, not used as separators (ex: "chr18:8,575,097-8,839,855" is ok).

### Value

GRanges object of the input strings

### See Also

`GRanges-class`

### Examples

      ran1 <- ranges_for_coords("chr1:2039-30239", with_names = TRUE)
      ran2 <- ranges_for_coords(c("chr1:2049-203902", "chrX:489249-1389389"),
                                meta_data_df = data.frame(dat = c("1", "X")))
      ran3 <- ranges_for_coords(c("chr1:2049-203902", "chrX:489249-1389389"),
                                with_names = TRUE,
                                meta_data_df = data.frame(dat = c("1", "X"),
                                               stringsAsFactors = FALSE))

[Package cicero version 1.12.0 Index]