In the following, the use of of the rt-arrest function will be applied to a MazF digestion assay from Zhang et al. 2019. Herein, 3 replicates of HEK293 mRNA were treated with FTO or mock treated and then subjected to a MazF digestion assay.
Usage
data(MazF_FTO)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 "-".