Usage
toGRanges(data, format=c("BED", "GFF", "MACS", "MACS2", "narrowPeak", "broadPeak", "others"), header=FALSE, comment.char="#", colNames=NULL, ...)
Arguments
data
BED, GFF, RangedData or any user defined dataset or their file path.
format
data format. If the data format is set to BED, GFF, narrowPeak or broadPeak,
please refer to http://genome.ucsc.edu/FAQ/FAQformat#format1 for column
order. "MACS" is for converting the excel output file from MACS1. "MACS2" is
for converting the output file from MACS2.
header
A logical value indicating whether the file contains the names of the
variables as its first line. If missing, the value is determined from the
file format: header is set to TRUE if and only if the first row contains one
fewer field than the number of columns.
comment.char
character: a character vector of length one containing a single character or
an empty string. Use "" to turn off the interpretation of comments
altogether.
colNames
If the data format is set to "others", colname must be defined. And the
colname must contain
space, start and end. The column name for the chromosome # should be named
as space.