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Subset of RDDs detected by JACUSA2 in HEK-293 untreated cells

Source: R/data.R
rdd.Rd

Subset of RDDs detected by JACUSA2 in HEK-293 untreated cells

Usage

data(rdd)

Format

a tibble with 18 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

  • score: Numeric value representing the test-statistc. Higher values indicate more divergent pileups

  • strand: Character representing strand information; "+", "-", or "."(no strand information available)

  • bases: Numeric tibble with representing counts for A, C, G, and T base calls.

  • cov: Numeric value indicating the read coverage for this site

  • 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 "-".

References

Piechotta, M.; Wyler, E.; Ohler, U.; Landthaler, M. & Dieterich, C. JACUSA: site-specific identification of RNA editing events from replicate sequencing data BMC Bioinformatics, Springer Nature, 2017 , 18

A dataset containing a subset of RNA DNA differences (RDDs) identified by JACUSA2 in untreated HEK-293 cells. The fields are as follows: