A function to re-align a GRanges object to a provided set of coordinates (either the TSS column or the TSS.fwd and TSS.rev columns)

A function to re-align a GRanges object to a provided set of coordinates (either the TSS column or the TSS.fwd and TSS.rev columns)

alignToTSS(granges, upstream = 0, downstream = 1)

Arguments

granges

A stranded GRanges object with a TSS column or TSS.rev and TSS.fwd columns
upstream

How many bases upstream of the TSS should the GRanges object by extended by? [Default: 0]
downstream

How many bases downstream of the TSS should the GRanges object by extended by? [Default: 1]

Value

GRanges aligned to the TSS column or to TSS.rev and TSS.fwd columns, and extended by upstream/downstream bp.