get_TSS_window: Return the interval.
In tinyheero/snpeffutils: Utility Functions for Working with SnpEff Data

Description Usage Arguments Details Value

This function will return a window that is upstream and downstream of every transcription start site in the snpeff.dt object.

1	get_TSS_window(snpeff.dt, upstream.len = 0, downstream.len = 2000)

`snpeff.dt`	SnpEff database dump data.table loaded through the load_snpeff_db_dump() function.
`upstream.len`	Integer value indicating the number of bases to include upstream of the transcription start site.
`downstream.len`	Integer value indicating the number of bases to include downstream of the transcription start site.

This function takes into account the strand the gene is on. So a downstream.len will apply to strand directionality the gene is. For instance, if gene A is on the - strand then the downstream.len applies "upstream" to the end coordinate of the gene (i.e. final downstream will be less than the TSS site). The final upstream and downstream coordinate columns are reported from a 5' respect regardless of what strand the gene is one (similar to how gene coordinates reported in general). The window includes the TSS in its range.

A data.table of containing the chr, upstream, downstream, and geneName of the around the TSS region.

tinyheero/snpeffutils documentation built on May 31, 2019, 3:36 p.m.