loadCoproData: Load CoPRO dataset

In Timothy-Barry/coproanalysis: Analyze CoPRO and Related Data

Description

This function returns the CoPRO data, a dataset containing a snapshot of the positions of all polymerases genome-wide. The data are ordered by column ID5. Morover, only trancscripts of width <= 500 and >= 18 are included in the data. Users can optionally specify chromStart and chomEnd. If a given chromosome has N

Usage

loadCoproData(chromStart = 0, chromEnd = 1, excludeXYM = TRUE)

Arguments

chromStart	a number between 0 and 1 indicating the start position on each chromosome.
chromEnd	a number between 0 and 1 indicating the end position on each chromosome.

Value

A genomicRanges object with the following columns: #'

seqnames

the name of the chromosome from which the transcript comes

ranges

the start and stop nucleotide of the transcript, where the nucleotides are numbered arbitrarily. Note that hydrogen-bonded nucleotides share the same identification number, and are distinguished by strand membership (i.e., + or -).

strand

the strand from which the nucleotide comes (i.e., plus + or minus -)

ID5,ID3

Numbers used to help identify the 5' and 3' ends of the transcript. Importantly, transcripts with the same ID5 start nucleotide share the same start nucleotide. Likewise, transcripts with the same ID3 share the same end nucleotide.

C

The number of capped reads of that transcript type.

U

The number of uncapped reads of that transcript type.

R

The number of total reads of that transcript type.

Source

Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers by Tome et al

Timothy-Barry/coproanalysis documentation built on Feb. 12, 2020, 7:33 a.m.