JACUSA2 output for rt-arrest on HIVRT condition in Zhou et. al 2018 data
Source:R/data.R
HIVRT_rt_arrest.RdZhou2018 et al. 2018 map RNA modification of pseudouridine \(\Psi\) by chemically modifying pseudouridines with carbodiimide (+CMC) and detecting arrest events that are induced by reverse transcription stops in high-throughput sequencing under 3 different conditions (HIVRT, SIIIMn, and SIIIMg). Result are for running JACUSA2 rt-arrest on processed pairwise +CMC and -CMC(control) data in HIVRT condition are presented.
Usage
data(HIVRT_rt_arrest)Format
a tibble with 22 elements:
id: Character string representing a unique identifier - created from contig, start, [end], and strand.
contig: Character string representing the contig of the variant
start: Numeric position of variant (>=0)
end: Numeric corresponds to "start + 1"
name: Character string. Name of used method call-2
pvalue: Numeric value representing the pvalue of the test.
strand: Character representing strand information; "+", "-", or "."(no strand information available)
arrest: Numeric tibble with representing counts for A, C, G, and T base calls from arrest reads.
through: Numeric tibble with representing counts for A, C, G, and T base calls from through reads.
bases: Numeric tibble with representing counts for A, C, G, and T base calls.
cov: Numeric value indicating the read coverage for this site
arrest_rate: Numeric tibble representing the arrest rate for each sample.
arrest_score: Numeric - test-statistic score.
backtrack1: Character - indicator if backtracking was used for condition 1.
backtrack2: Character - indicator if backtracking was used for condition 2.
backtrackP: Character - indicator if backtracking was used for condition pooled condition.
reset1: Character - indicator if default estimation was unstable with for condition 1.
reset2: Character - indicator if default estimation was unstable with for condition 2.
resetP: Character - indicator if default estimation was unstable with for pooled condition.
info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".