JACUSA2helper: Post-processing for JACUSA2 output

#' Subset of RDDs detected by JACUSA2 in HEK-293 untreated cells
#'
#' @docType data
#' 
#' @usage data(rdd)
#'
#' @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:
#' @format a tibble with 18 elements:
#' \itemize{
#'    \item id: Character string representing a unique identifier - created from contig, start, [end], and strand.
#'		\item contig: Character string representing the contig of the variant
#'		\item start: Numeric position of variant (>=0)
#'		\item end: Numeric corresponds to "start + 1"
#'		\item name: Character string. Name of used method \emph{call-2}
#'		\item score: Numeric value representing the test-statistc. Higher values indicate more divergent pileups
#'		\item strand: Character representing strand information; "+", "-", or "."(no strand information available)
#'		\item bases: Numeric tibble with representing counts for A, C, G, and T base calls.
#'    \item cov: Numeric value indicating the read coverage for this site
#'    \item backtrack1: Character - indicator if backtracking was used for condition 1.
#'    \item backtrack2: Character - indicator if backtracking was used for condition 2.
#'    \item backtrackP: Character - indicator if backtracking was used for condition pooled condition.
#'    \item reset1: Character - indicator if default estimation was unstable with for condition 1.
#'    \item reset2: Character - indicator if default estimation was unstable with for condition 2.
#'    \item resetP: Character - indicator if default estimation was unstable with for pooled condition.
#'		\item info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
#'		\item filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
#'		\item ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".
#' }
"rdd"

#' Subset of RRDs detected by JACUSA2 in HEK-293 ADAR KD and untreated cells
#' 
#' Data extrated from:
#' 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
#' 
#' @docType data
#' 
#' @usage data(rrd)
#'
#' @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 RNA differences (RRDs) identified by JACUSA2 in ADAR KD and untreated HEK-293 cells. 
#' The fields are as follows:
#' @format a tibble with 18 elements:
#' \itemize{
#'    \item id: Character string representing a unique identifier - created from contig, start, [end], and strand.
#'		\item contig: Character string representing the contig of the variant
#'		\item start: Numeric position of variant (>=0)
#'		\item end: Numeric corresponds to "start + 1"
#'		\item name: Character string. Name of used method \emph{call-2}
#'		\item score: Numeric value representing the test-statistc. Higher values indicate more divergent pileups
#'		\item strand: Character representing strand information; "+", "-", or "."(no strand information available)
#'		\item bases: Numeric tibble with representing counts for A, C, G, and T base calls.
#'    \item cov: Numeric value indicating the read coverage for this site
#'    \item backtrack1: Character - indicator if backtracking was used for condition 1.
#'    \item backtrack2: Character - indicator if backtracking was used for condition 2.
#'    \item backtrackP: Character - indicator if backtracking was used for condition pooled condition.
#'    \item reset1: Character - indicator if default estimation was unstable with for condition 1.
#'    \item reset2: Character - indicator if default estimation was unstable with for condition 2.
#'    \item resetP: Character - indicator if default estimation was unstable with for pooled condition.
#'		\item info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
#'		\item filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
#'		\item ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".
#' }
"rrd"

#' JACUSA2 output for rt-arrest on HIVRT condition in Zhou et. al 2018 data
#' 
#' Zhou2018 et al. 2018 map RNA modification of pseudouridine \eqn{\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.
#'
#' Check Section "Reverse transcriptase arrest events" in 
#' https://github.com/dieterich-lab/JACUSA2/blob/master/manual/manual.pdf
#' for details on pre-processing and mapping primary sequencing data.
#' 
#' @docType data
#' 
#' @usage data(HIVRT_rt_arrest)
#' 
#' @references Zhou, K. I.; Clark, W. C.; Pan, D. W.; Eckwahl, M. J.; Dai, Q. & Pan, T.
#' Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing 
#' RNA Biology, Informa UK Limited, 2018 , 15 , 892-900
#' 
#' @format a tibble with 22 elements:
#' \itemize{
#'    \item id: Character string representing a unique identifier - created from contig, start, [end], and strand.
#'		\item contig: Character string representing the contig of the variant
#'		\item start: Numeric position of variant (>=0)
#'		\item end: Numeric corresponds to "start + 1"
#'		\item name: Character string. Name of used method \emph{call-2}
#'		\item pvalue: Numeric value representing the pvalue of the test.
#'		\item strand: Character representing strand information; "+", "-", or "."(no strand information available)
#'		\item arrest: Numeric tibble with representing counts for A, C, G, and T base calls from arrest reads.
#'		\item through: Numeric tibble with representing counts for A, C, G, and T base calls from through reads.
#'		\item bases: Numeric tibble with representing counts for A, C, G, and T base calls.
#'    \item cov: Numeric value indicating the read coverage for this site
#'    \item arrest_rate: Numeric tibble representing the arrest rate for each sample.
#'    \item arrest_score: Numeric - test-statistic score.
#'    \item backtrack1: Character - indicator if backtracking was used for condition 1.
#'    \item backtrack2: Character - indicator if backtracking was used for condition 2.
#'    \item backtrackP: Character - indicator if backtracking was used for condition pooled condition.
#'    \item reset1: Character - indicator if default estimation was unstable with for condition 1.
#'    \item reset2: Character - indicator if default estimation was unstable with for condition 2.
#'    \item resetP: Character - indicator if default estimation was unstable with for pooled condition.
#'		\item info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
#'		\item filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
#'		\item ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".
#' }
"HIVRT_rt_arrest"

#' JACUSA2 output for rt-arrest on SIIIRTMg condition in Zhou et. al 2018 data
#' 
#' Zhou2018 et al. 2018 map RNA modification of pseudouridine \eqn{\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 SIIIRTMg condition are presented.
#'
#' Check Section "Reverse transcriptase arrest events" in 
#' https://github.com/dieterich-lab/JACUSA2/blob/master/manual/manual.pdf
#' for details on pre-processing and mapping primary sequencing data.
#' 
#' @docType data
#' 
#' @usage data(SIIIRTMg_rt_arrest)
#' 
#' @references Zhou, K. I.; Clark, W. C.; Pan, D. W.; Eckwahl, M. J.; Dai, Q. & Pan, T.
#' Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing 
#' RNA Biology, Informa UK Limited, 2018 , 15 , 892-900
#' 
#' @format a tibble with 22 elements:
#' \itemize{
#'    \item id: Character string representing a unique identifier - created from contig, start, [end], and strand.
#'		\item contig: Character string representing the contig of the variant
#'		\item start: Numeric position of variant (>=0)
#'		\item end: Numeric corresponds to "start + 1"
#'		\item name: Character string. Name of used method \emph{call-2}
#'		\item pvalue: Numeric value representing the pvalue of the test.
#'		\item strand: Character representing strand information; "+", "-", or "."(no strand information available)
#'		\item arrest: Numeric tibble with representing counts for A, C, G, and T base calls from arrest reads.
#'		\item through: Numeric tibble with representing counts for A, C, G, and T base calls from through reads.
#'		\item bases: Numeric tibble with representing counts for A, C, G, and T base calls.
#'    \item cov: Numeric value indicating the read coverage for this site
#'    \item arrest_rate: Numeric tibble representing the arrest rate for each sample.
#'    \item arrest_score: Numeric - test-statistic score.
#'    \item backtrack1: Character - indicator if backtracking was used for condition 1.
#'    \item backtrack2: Character - indicator if backtracking was used for condition 2.
#'    \item backtrackP: Character - indicator if backtracking was used for condition pooled condition.
#'    \item reset1: Character - indicator if default estimation was unstable with for condition 1.
#'    \item reset2: Character - indicator if default estimation was unstable with for condition 2.
#'    \item resetP: Character - indicator if default estimation was unstable with for pooled condition.
#'		\item info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
#'		\item filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
#'		\item ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".
#' }
"SIIIRTMg_rt_arrest"

#' JACUSA2 output for rt-arrest on SIIIRTMn condition in Zhou et. al 2018 data
#' 
#' Zhou2018 et al. 2018 map RNA modification of pseudouridine \eqn{\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 SIIIRTMn condition are presented.
#'
#' Check Section "Reverse transcriptase arrest events" 
#' https://github.com/dieterich-lab/JACUSA2/blob/master/manual/manual.pdf
#' for details on pre-processing and mapping primary sequencing data.
#' 
#' @docType data
#'
#' @usage data(SIIIRTMn_rt_arrest)
#' 
#' @references Zhou, K. I.; Clark, W. C.; Pan, D. W.; Eckwahl, M. J.; Dai, Q. & Pan, T.
#' Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing 
#' RNA Biology, Informa UK Limited, 2018 , 15 , 892-900
#' 
#' @format a tibble with 22 elements:
#' \itemize{
#'    \item id: Character string representing a unique identifier - created from contig, start, [end], and strand.
#'		\item contig: Character string representing the contig of the variant
#'		\item start: Numeric position of variant (>=0)
#'		\item end: Numeric corresponds to "start + 1"
#'		\item name: Character string. Name of used method \emph{call-2}
#'		\item pvalue: Numeric value representing the pvalue of the test.
#'		\item strand: Character representing strand information; "+", "-", or "."(no strand information available)
#'		\item arrest: Numeric tibble with representing counts for A, C, G, and T base calls from arrest reads.
#'		\item through: Numeric tibble with representing counts for A, C, G, and T base calls from through reads.
#'		\item bases: Numeric tibble with representing counts for A, C, G, and T base calls.
#'    \item cov: Numeric value indicating the read coverage for this site
#'    \item arrest_rate: Numeric tibble representing the arrest rate for each sample.
#'    \item arrest_score: Numeric - test-statistic score.
#'    \item backtrack1: Character - indicator if backtracking was used for condition 1.
#'    \item backtrack2: Character - indicator if backtracking was used for condition 2.
#'    \item backtrackP: Character - indicator if backtracking was used for condition pooled condition.
#'    \item reset1: Character - indicator if default estimation was unstable with for condition 1.
#'    \item reset2: Character - indicator if default estimation was unstable with for condition 2.
#'    \item resetP: Character - indicator if default estimation was unstable with for pooled condition.
#'		\item info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
#'		\item filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
#'		\item ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".
#' }
"SIIIRTMn_rt_arrest"

#' Combined JACUSA2 output for rt-arrest on all conditions in Zhou et. al 2018 data
#' 
#' Zhou2018 et al. 2018 map RNA modification of pseudouridine \eqn{\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). 
#' A combined version of all conditions and their pairwise +CMC and -CMC(control) comparisons is presented.
#' The data structure contains an additional field "meta_condition" that corresponds and identifies the 
#' condition from Zhou 2018: 
#' \itemize{
#'   \item HIVRT, 
#'   \item SIIIMn, and
#'   \item SIIIMg.
#' }
#' This dataset exemplifies the usefullness of combining multiple pairwise comparisons and make them distinguishable by
#' "meta" field.
#' 
#' Check Section "Reverse transcriptase arrest events" in 
#' https://github.com/dieterich-lab/JACUSA2/blob/master/manual/manual.pdf
#' for details on pre-processing and mapping primary sequencing data.
#' 
#' @docType data
#' 
#' @usage data(Zhou2018_rt_arrest)
#' 
#' @references Zhou, K. I.; Clark, W. C.; Pan, D. W.; Eckwahl, M. J.; Dai, Q. & Pan, T.
#' Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing 
#' RNA Biology, Informa UK Limited, 2018 , 15 , 892-900
#' 
#' @format a tibble with 23 elements:
#' \itemize{
#'    \item id: Character string representing a unique identifier - created from contig, start, [end], and strand.
#'		\item contig: Character string representing the contig of the variant
#'		\item start: Numeric position of variant (>=0)
#'		\item end: Numeric corresponds to "start + 1"
#'		\item name: Character string. Name of used method \emph{call-2}
#'		\item pvalue: Numeric value representing the pvalue of the test.
#'		\item strand: Character representing strand information; "+", "-", or "."(no strand information available)
#'		\item arrest: Numeric tibble with representing counts for A, C, G, and T base calls from arrest reads.
#'		\item through: Numeric tibble with representing counts for A, C, G, and T base calls from through reads.
#'		\item bases: Numeric tibble with representing counts for A, C, G, and T base calls.
#'    \item cov: Numeric value indicating the read coverage for this site
#'    \item arrest_rate: Numeric tibble representing the arrest rate for each sample.
#'    \item arrest_score: Numeric - test-statistic score.
#'    \item backtrack1: Character - indicator if backtracking was used for condition 1.
#'    \item backtrack2: Character - indicator if backtracking was used for condition 2.
#'    \item backtrackP: Character - indicator if backtracking was used for condition pooled condition.
#'    \item reset1: Character - indicator if default estimation was unstable with for condition 1.
#'    \item reset2: Character - indicator if default estimation was unstable with for condition 2.
#'    \item resetP: Character - indicator if default estimation was unstable with for pooled condition.
#'		\item info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
#'		\item filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
#'		\item ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".
#'    \item meta: Character string indicating the dataset. Here: "HIVRT", "SIIIRTMn", or "SIIIRTMn".
#' }
"Zhou2018_rt_arrest"

#' JACUSA2 output for call-2 on HIVRT condition in Zhou et. al 2018 data
#' 
#' Zhou2018 et al. 2018 map RNA modification of pseudouridine \eqn{\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 call-2 on processed pairwise +CMC and -CMC(control) data in HIVRT condition are presented.
#'
#' Check Section "Reverse transcriptase arrest events" in 
#' https://github.com/dieterich-lab/JACUSA2/blob/master/manual/manual.pdf
#' for details on pre-processing and mapping primary sequencing data.
#' 
#' @docType data
#' 
#' @usage data(HIVRT_call2)
#' 
#' @references Zhou, K. I.; Clark, W. C.; Pan, D. W.; Eckwahl, M. J.; Dai, Q. & Pan, T.
#' Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing 
#' RNA Biology, Informa UK Limited, 2018 , 15 , 892-900
#' 
#' @format a tibble with 18 elements:
#' \itemize{
#'    \item id: Character string representing a unique identifier - created from contig, start, [end], and strand.
#'		\item contig: Character string representing the contig of the variant
#'		\item start: Numeric position of variant (>=0)
#'		\item end: Numeric corresponds to "start + 1"
#'		\item name: Character string. Name of used method \emph{call-2}
#'		\item score: Numeric value representing the test-statistc. Higher values indicate more divergent pileups
#'		\item strand: Character representing strand information; "+", "-", or "."(no strand information available)
#'		\item bases: Numeric tibble with representing counts for A, C, G, and T base calls.
#'    \item cov: Numeric value indicating the read coverage for this site
#'    \item backtrack1: Character - indicator if backtracking was used for condition 1.
#'    \item backtrack2: Character - indicator if backtracking was used for condition 2.
#'    \item backtrackP: Character - indicator if backtracking was used for condition pooled condition.
#'    \item reset1: Character - indicator if default estimation was unstable with for condition 1.
#'    \item reset2: Character - indicator if default estimation was unstable with for condition 2.
#'    \item resetP: Character - indicator if default estimation was unstable with for pooled condition.
#'		\item info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
#'		\item filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
#'		\item ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".
#' }
"HIVRT_call2"

#' JACUSA2 output for call-22 on SIIIRTMg condition in Zhou et. al 2018 data
#' 
#' Zhou2018 et al. 2018 map RNA modification of pseudouridine \eqn{\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 call-2 on processed pairwise +CMC and -CMC(control) data in SIIIRTMg condition are presented.
#'
#' Check Section "Reverse transcriptase arrest events" 
#' https://github.com/dieterich-lab/JACUSA2/blob/master/manual/manual.pdf
#' for details on pre-processing and mapping primary sequencing data.
#' 
#' @docType data
#' 
#' @usage data(SIIIRTMg_call2)
#' 
#' @references Zhou, K. I.; Clark, W. C.; Pan, D. W.; Eckwahl, M. J.; Dai, Q. & Pan, T.
#' Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing 
#' RNA Biology, Informa UK Limited, 2018 , 15 , 892-900
#' 
#' @format a tibble with 18 elements:
#' \itemize{
#'    \item id: Character string representing a unique identifier - created from contig, start, [end], and strand.
#'		\item contig: Character string representing the contig of the variant
#'		\item start: Numeric position of variant (>=0)
#'		\item end: Numeric corresponds to "start + 1"
#'		\item name: Character string. Name of used method \emph{call-2}
#'		\item score: Numeric value representing the test-statistc. Higher values indicate more divergent pileups
#'		\item strand: Character representing strand information; "+", "-", or "."(no strand information available)
#'		\item bases: Numeric tibble with representing counts for A, C, G, and T base calls.
#'    \item cov: Numeric value indicating the read coverage for this site
#'    \item backtrack1: Character - indicator if backtracking was used for condition 1.
#'    \item backtrack2: Character - indicator if backtracking was used for condition 2.
#'    \item backtrackP: Character - indicator if backtracking was used for condition pooled condition.
#'    \item reset1: Character - indicator if default estimation was unstable with for condition 1.
#'    \item reset2: Character - indicator if default estimation was unstable with for condition 2.
#'    \item resetP: Character - indicator if default estimation was unstable with for pooled condition.
#'		\item info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
#'		\item filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
#'		\item ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".
#' }
"SIIIRTMg_call2"

#' JACUSA2 output for call-2 on SIIIRTMn condition in Zhou et. al 2018 data
#' 
#' Zhou2018 et al. 2018 map RNA modification of pseudouridine \eqn{\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 call-2 on processed pairwise +CMC and -CMC(control) data in SIIIRTMn condition are presented.
#'
#' Check Section "Reverse transcriptase arrest events" in 
#' https://github.com/dieterich-lab/JACUSA2/blob/master/manual/manual.pdf
#' for details on pre-processing and mapping primary sequencing data.
#' 
#' @docType data
#'
#' @usage data(SIIIRTMn_call2)
#' 
#' @references Zhou, K. I.; Clark, W. C.; Pan, D. W.; Eckwahl, M. J.; Dai, Q. & Pan, T.
#' Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing 
#' RNA Biology, Informa UK Limited, 2018 , 15 , 892-900
#' 
#' @format a tibble with 18 elements:
#' \itemize{
#'    \item id: Character string representing a unique identifier - created from contig, start, [end], and strand.
#'		\item contig: Character string representing the contig of the variant
#'		\item start: Numeric position of variant (>=0)
#'		\item end: Numeric corresponds to "start + 1"
#'		\item name: Character string. Name of used method \emph{call-2}
#'		\item score: Numeric value representing the test-statistc. Higher values indicate more divergent pileups
#'		\item strand: Character representing strand information; "+", "-", or "."(no strand information available)
#'		\item bases: Numeric tibble with representing counts for A, C, G, and T base calls.
#'    \item cov: Numeric value indicating the read coverage for this site
#'    \item backtrack1: Character - indicator if backtracking was used for condition 1.
#'    \item backtrack2: Character - indicator if backtracking was used for condition 2.
#'    \item backtrackP: Character - indicator if backtracking was used for condition pooled condition.
#'    \item reset1: Character - indicator if default estimation was unstable with for condition 1.
#'    \item reset2: Character - indicator if default estimation was unstable with for condition 2.
#'    \item resetP: Character - indicator if default estimation was unstable with for pooled condition.
#'		\item info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
#'		\item filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
#'		\item ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".
#' }
"SIIIRTMn_call2"

#' Combined JACUSA2 output for call-2 on all conditions in Zhou et. al 2018 data
#' 
#' Zhou2018 et al. 2018 map RNA modification of pseudouridine \eqn{\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). 
#' A combined version of all conditions and their pairwise +CMC and -CMC(control) comparisons is presented.
#' The data structure contains an additional field "meta_condition" that corresponds and identifies the 
#' condition from Zhou 2018: 
#' \itemize{
#'   \item HIVRT, 
#'   \item SIIIMn, and
#'   \item SIIIMg.
#' }
#' This dataset exemplifies the usefullness of combining multiple pairwise comparisons and make them distinguishable by
#' "meta" field.
#' 
#' @docType data
#' 
#' @usage data(Zhou2018_call2)
#' 
#' @references Zhou, K. I.; Clark, W. C.; Pan, D. W.; Eckwahl, M. J.; Dai, Q. & Pan, T.
#' Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing 
#' RNA Biology, Informa UK Limited, 2018 , 15 , 892-900
#' 
#' @format a tibble with 19 elements:
#' \itemize{
#'    \item id: Character string representing a unique identifier - created from contig, start, [end], and strand.
#'		\item contig: Character string representing the contig of the variant
#'		\item start: Numeric position of variant (>=0)
#'		\item end: Numeric corresponds to "start + 1"
#'		\item name: Character string. Name of used method \emph{call-2}
#'		\item score: Numeric value representing the test-statistc. Higher values indicate more divergent pileups
#'		\item strand: Character representing strand information; "+", "-", or "."(no strand information available)
#'		\item bases: Numeric tibble with representing counts for A, C, G, and T base calls.
#'    \item cov: Numeric value indicating the read coverage for this site
#'    \item backtrack1: Character - indicator if backtracking was used for condition 1.
#'    \item backtrack2: Character - indicator if backtracking was used for condition 2.
#'    \item backtrackP: Character - indicator if backtracking was used for condition pooled condition.
#'    \item reset1: Character - indicator if default estimation was unstable with for condition 1.
#'    \item reset2: Character - indicator if default estimation was unstable with for condition 2.
#'    \item resetP: Character - indicator if default estimation was unstable with for pooled condition.
#'		\item info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
#'		\item filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
#'		\item ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".
#'    \item meta: Character string indicating the dataset. Here: "HIVRT", "SIIIRTMn", or "SIIIRTMn".
#' }
"Zhou2018_call2"

#' rRNA modification map of rRNAs according to Taika et al.
#' 
#' Data (18S, 28S, and 5.8S) has been extracted from retrieved from PMID: 30202881.
#'
#' @docType data
#' 
#' @usage data(rnam)
#' 
#' @references Landscape of the complete RNA chemical modifications in the human 80S ribosome
#'             Masato Taoka, Yuko Nobe, Yuka Yamaki, Ko Sato, Hideaki Ishikawa, 
#'             Keiichi Izumikawa, Yoshio Yamauchi, Kouji Hirota, Hiroshi Nakayama, 
#'             Nobuhiro Takahashi et al. 
#'             Nucleic Acids Research, Volume 46, Issue 18, 12 October 2018, Pages 9289–9298, 
#'             https://doi.org/10.1093/nar/gky811
#' 
#' @format a data.frame with 3 elements:
#' \itemize{
#'   \item rrna: String, either "18S", "28S", or "5.8S"
#'   \item pos: Numeric 1-index position.
#'   \item base: String, reference base(A, C, G, T) or modification(ac4C, AM, Cm, 
#'         Gm, m1A, m1acp3pusU, m3U, m5C, m62A, m6A, m7G, ND, psU, psUm, Um)
#' }
"rnam"

#' DART-seq from Meyer 2019
#' 
#' A complementary genetic approach is an extension of the TRIBE technique called DART-seq Meyer 2019.
#' Beyer applied DART-seq on HEK293 cells where the APOBEC domain was fused to the YTH domain from human YTHDF2 (WT and mutated).
#' In essence, new C-to-U editing events that are significantly enriched in the YTHDF2-WT, 
#' but not in the binding domain mutant are bona fide candidates for m6A RNA modification
#' 
#' @docType data
#' 
#' @usage data(DARTseq)
#' 
#' @references Meyer, Kate D., Nature methods, December 19, 2019
#' 
#' @format a tibble with 18 elements:
#' \itemize{
#'    \item id: Character string representing a unique identifier - created from contig, start, [end], and strand.
#'		\item contig: Character string representing the contig of the variant
#'		\item start: Numeric position of variant (>=0)
#'		\item end: Numeric corresponds to "start + 1"
#'		\item name: Character string. Name of used method \emph{call-2}
#'		\item score: Numeric value representing the test-statistc. Higher values indicate more divergent pileups
#'		\item strand: Character representing strand information; "+", "-", or "."(no strand information available)
#'		\item bases: Numeric tibble with representing counts for A, C, G, and T base calls.
#'    \item cov: Numeric value indicating the read coverage for this site
#'    \item backtrack1: Character - indicator if backtracking was used for condition 1.
#'    \item backtrack2: Character - indicator if backtracking was used for condition 2.
#'    \item backtrackP: Character - indicator if backtracking was used for condition pooled condition.
#'    \item reset1: Character - indicator if default estimation was unstable with for condition 1.
#'    \item reset2: Character - indicator if default estimation was unstable with for condition 2.
#'    \item resetP: Character - indicator if default estimation was unstable with for pooled condition.
#'		\item info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
#'		\item filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
#'		\item ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".
#' }
"DARTseq"

#' MazF_FTO from Zhang et al. 2019
#' 
#' 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.
#' 
#' @docType data
#' 
#' @usage data(MazF_FTO)
#' 
#' @references Zhang, Zhang and Chen, Li-Qian and Zhao, Yu-Li and Yang, 
#'             Cai-Guang and Roundtree, Ian A. and Zhang, Zijie and Ren, Jian and 
#'             Xie, Wei and He, Chuan and Luo, Guan-Zheng
#'             Science advances, July 5, 2019
#'             
#' 
#' @format a tibble with 22 elements:
#' \itemize{
#'    \item id: Character string representing a unique identifier - created from contig, start, [end], and strand.
#'		\item contig: Character string representing the contig of the variant
#'		\item start: Numeric position of variant (>=0)
#'		\item end: Numeric corresponds to "start + 1"
#'		\item name: Character string. Name of used method \emph{call-2}
#'		\item pvalue: Numeric value representing the pvalue of the test.
#'		\item strand: Character representing strand information; "+", "-", or "."(no strand information available)
#'		\item arrest: Numeric tibble with representing counts for A, C, G, and T base calls from arrest reads.
#'		\item through: Numeric tibble with representing counts for A, C, G, and T base calls from through reads.
#'		\item bases: Numeric tibble with representing counts for A, C, G, and T base calls.
#'    \item cov: Numeric value indicating the read coverage for this site
#'    \item arrest_rate: Numeric tibble representing the arrest rate for each sample.
#'    \item arrest_score: Numeric - test-statistic score.
#'    \item backtrack1: Character - indicator if backtracking was used for condition 1.
#'    \item backtrack2: Character - indicator if backtracking was used for condition 2.
#'    \item backtrackP: Character - indicator if backtracking was used for condition pooled condition.
#'    \item reset1: Character - indicator if default estimation was unstable with for condition 1.
#'    \item reset2: Character - indicator if default estimation was unstable with for condition 2.
#'    \item resetP: Character - indicator if default estimation was unstable with for pooled condition.
#'		\item info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
#'		\item filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
#'		\item ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".
#' }
"MazF_FTO"


#' m6a predictions from 3 miCLIP experiments
#' 
#' Genomic coordinates (excluding Y chromosome) for m6a sites from 3 experiments: 
#' \itemize{
#'   \item Boulias et al. 2019,
#'   \item Koh et al. 2019, and
#'   \item Koertel et al. 2021.
#' }
#' 
#' @docType data
#' 
#' @usage data(m6a_miclip)
#' 
#' @references Koh CWQ, Goh YT, Goh WSS. Atlas of quantitative single-base-resolution n6-methyl-adenine methylomes. Nat Commun. 2019; 10:5636. https://doi.org/10.1038/s41467-019-13561-z.
#' @references Boulias K, Toczydłowska-Socha D, Hawley BR, Liberman N, Takashima K, Zaccara S, Guez T, Vasseur J-J, Debart F, Aravind L, Jaffrey SR, Greer EL. Identification of the m, javax.xml.bind.jaxbelement@3155288a, am methyltransferase pcif1 reveals the location and functions of m, javax.xml.bind.jaxbelement@72f29a24, am in the transcriptome. Mol Cell. 2019; 75:631–6438. https://doi.org/10.1016/j.molcel.2019.06.006.
#' @references Körtel N, Rücklé C, Zhou Y, Busch A, Hoch-Kraft P, Sutandy FXR, Haase J, Pradhan M, Musheev M, Ostareck D, Ostareck-Lederer A, Dieterich C, Hüttelmaier S, Niehrs C, Rausch O, Dominissini D, König J, Zarnack K. Deep and accurate detection of m6a RNA modifications using miclip2 and m6aboost machine learning. Nucleic Acids Res. 2021; 49:92. https://doi.org/10.1093/nar/gkab485.
#' 
#' @format a GRanges object:
#' \itemize{
#'    \item experiments: Character string. Possible values, all combinations of: Boulias, Koh, and Koertel
#'		\item region ref: Character string. Coordinates, format: "chr:start-end:strand".
#' }
"m6a_miclip"

#' Non-negative matrix factorization on m6a predictions from 3 miCLIP experiments
#' 
#' @seealso JACUSA2helper::m6a_miclip.
#' 
#' Predictions are based on data from:
#' \itemize{
#'   \item Boulias et al. 2019,
#'   \item Koh et al. 2019, and
#'   \item Koertel et al. 2021.
#' }
#' 
#' @docType data
#' 
#' @usage data(m6a_nmf_results)
#'
#' @details description of list items:
#' \itemize{
#'  \item{"estim_r"}{Factorizations for `x`}
#'  \item{"nmf_matrix"}{Factorization of `x` with `r` that maximizes `estim_r$measures$silhouette.consensus` and `estim_r$measures$cophenetic`}
#'  \item{"chosen_rank"}{Optimal rank}
#'  \item{"chosen_pattern"}{The pattern that has the highest score}
##'  \item{"reduced_coef"}{Reduced coefficient matrix.}
#' }
#'
#' @references Koh CWQ, Goh YT, Goh WSS. Atlas of quantitative single-base-resolution n6-methyl-adenine methylomes. Nat Commun. 2019; 10:5636. https://doi.org/10.1038/s41467-019-13561-z.
#' @references Boulias K, Toczydłowska-Socha D, Hawley BR, Liberman N, Takashima K, Zaccara S, Guez T, Vasseur J-J, Debart F, Aravind L, Jaffrey SR, Greer EL. Identification of the m, javax.xml.bind.jaxbelement@3155288a, am methyltransferase pcif1 reveals the location and functions of m, javax.xml.bind.jaxbelement@72f29a24, am in the transcriptome. Mol Cell. 2019; 75:631–6438. https://doi.org/10.1016/j.molcel.2019.06.006.
#' @references Körtel N, Rücklé C, Zhou Y, Busch A, Hoch-Kraft P, Sutandy FXR, Haase J, Pradhan M, Musheev M, Ostareck D, Ostareck-Lederer A, Dieterich C, Hüttelmaier S, Niehrs C, Rausch O, Dominissini D, König J, Zarnack K. Deep and accurate detection of m6a RNA modifications using miclip2 and m6aboost machine learning. Nucleic Acids Res. 2021; 49:92. https://doi.org/10.1093/nar/gkab485.
#'
#' @format a list with results from NMF
"m6a_nmf_results"

#' Non-negative matrix factorization on m6a predictions from 3 miCLIP experiments
#' 
#' @seealso JACUSA2helper::m6a_miclip.
#' 
#' Predictions are based on data from:
#' \itemize{
#'   \item Boulias et al. 2019,
#'   \item Koh et al. 2019, and
#'   \item Koertel et al. 2021.
#' }
#' 
#' @docType data
#' 
#' @usage data(m6a_nmf_results)
#'
#' @details description of list items:
#' \itemize{
#'  \item{"estim_r"}{Factorizations for `x`}
#'  \item{"nmf_matrix"}{Factorization of `x` with `r` that maximizes `estim_r$measures$silhouette.consensus` and `estim_r$measures$cophenetic`}
#'  \item{"chosen_rank"}{Optimal rank}
#'  \item{"chosen_pattern"}{The pattern that has the highest score}
##'  \item{"reduced_coef"}{Reduced coefficient matrix.}
#' }
#'
#' @references Koh CWQ, Goh YT, Goh WSS. Atlas of quantitative single-base-resolution n6-methyl-adenine methylomes. Nat Commun. 2019; 10:5636. https://doi.org/10.1038/s41467-019-13561-z.
#' @references Boulias K, Toczydłowska-Socha D, Hawley BR, Liberman N, Takashima K, Zaccara S, Guez T, Vasseur J-J, Debart F, Aravind L, Jaffrey SR, Greer EL. Identification of the m, javax.xml.bind.jaxbelement@3155288a, am methyltransferase pcif1 reveals the location and functions of m, javax.xml.bind.jaxbelement@72f29a24, am in the transcriptome. Mol Cell. 2019; 75:631–6438. https://doi.org/10.1016/j.molcel.2019.06.006.
#' @references Körtel N, Rücklé C, Zhou Y, Busch A, Hoch-Kraft P, Sutandy FXR, Haase J, Pradhan M, Musheev M, Ostareck D, Ostareck-Lederer A, Dieterich C, Hüttelmaier S, Niehrs C, Rausch O, Dominissini D, König J, Zarnack K. Deep and accurate detection of m6a RNA modifications using miclip2 and m6aboost machine learning. Nucleic Acids Res. 2021; 49:92. https://doi.org/10.1093/nar/gkab485.
#'
#' @format a list with results from NMF
"m6a_nmf_reduced"