read.meland.tags: Read modified BED tag alignment file that contains variable...
In spp: ChIP-Seq Processing Pipeline

Description Usage Arguments Value

Reads in an extended BED tag alignment file. An example line given below: 49 . U1 . 1 . . 23 chr2 -234567 The line above specifies a 23-bp portion of the tag tag with id 49 was aligned with 1 mismatch to the negative strand of chr2 at position 234567.

1	read.meland.tags(filename, read.tag.names = F, fix.chromosome.names = T)

`filename`	name of the extended BED file
`read.tag.names`	whether to read in tag names
`fix.chromosome.names`	whether to remove ".fa" from the sequence name ends.

`tags`	A vector of 5' tag coordinates, with negative values corresponding to tags mapped to the negative strand.
`quality`	Quality expressed as a float x.y, where x is tag.length - aligned.tag.portion.length, and y is the number of mismatches (must be less than 10).
`names`	Tag names, if `read.tag.names` was set