R/data.R

In bridger2: Genome-Wide RNA Degradation Analysis Using BRIC-Seq Data

#' test BRIC-seq dataset for RNA half-life comparison
#'
#' A dataset containing the RPKM for each time point and information column
#'  about 200 genes. The variables are as follows:
#'
#' @format A data frame with 200 rows and 20 variables:
#' \describe{
#'   \item{gr_id}{Group id}
#'   \item{symbol}{Gene symbol}
#'   \item{accession_id}{Gene accession id (RefSeq)}
#'   \item{locus}{Genome locus}
#'   \item{CTRL_1_0h}{RPKM value at 0h in control condition}
#'   \item{CTRL_1_1h}{RPKM value at 1h in control condition}
#'   \item{CTRL_1_2h}{RPKM value at 2h in control condition}
#'   \item{CTRL_1_4h}{RPKM value at 4h in control condition}
#'   \item{CTRL_1_8h}{RPKM value at 8h in control condition}
#'   \item{CTRL_1_12h}{RPKM value at 12h in control condition}
#'   \item{gr_id}{Group id}
#'   \item{symbol}{Gene symbol}
#'   \item{accession_id}{Gene accession id (RefSeq)}
#'   \item{locus}{Genome locus}
#'   \item{KD_1_0h}{RPKM value at 0h in knockdown condition}
#'   \item{KD_1_1h}{RPKM value at 1h in knockdown condition}
#'   \item{KD_1_2h}{RPKM value at 2h in knockdown condition}
#'   \item{KD_1_4h}{RPKM value at 4h in knockdown condition}
#'   \item{KD_1_8h}{RPKM value at 8h in knockdown condition}
#'   \item{KD_1_12h}{RPKM value at 12h in knockdown condition}
#' }
"RNA_halflife_comparison"


#' test BRIC-seq dataset for RNA half-life comparison using House-keeping genes.
#'
#' A dataset containing the RPKM for each time point and information column
#'  about 200 genes + house-keeping genes. The variables are as follows:
#'
#' @format A data frame with 200 rows and 20 variables:
#' \describe{
#'   \item{gr_id}{Group id}
#'   \item{symbol}{Gene symbol}
#'   \item{accession_id}{Gene accession id (RefSeq)}
#'   \item{locus}{Genome locus}
#'   \item{CTRL_1_0h}{RPKM value at 0h in control condition}
#'   \item{CTRL_1_1h}{RPKM value at 1h in control condition}
#'   \item{CTRL_1_2h}{RPKM value at 2h in control condition}
#'   \item{CTRL_1_4h}{RPKM value at 4h in control condition}
#'   \item{CTRL_1_8h}{RPKM value at 8h in control condition}
#'   \item{CTRL_1_12h}{RPKM value at 12h in control condition}
#'   \item{gr_id}{Group id}
#'   \item{symbol}{Gene symbol}
#'   \item{accession_id}{Gene accession id (RefSeq)}
#'   \item{locus}{Genome locus}
#'   \item{KD_1_0h}{RPKM value at 0h in knockdown condition}
#'   \item{KD_1_1h}{RPKM value at 1h in knockdown condition}
#'   \item{KD_1_2h}{RPKM value at 2h in knockdown condition}
#'   \item{KD_1_4h}{RPKM value at 4h in knockdown condition}
#'   \item{KD_1_8h}{RPKM value at 8h in knockdown condition}
#'   \item{KD_1_12h}{RPKM value at 12h in knockdown condition}
#' }
"RNA_halflife_comparison_HK"


#' test BRIC-seq dataset for p-value estimation using grubbs test
#'
#' A dataset containing the RPKM for each time point and information column
#'  about 200 genes. The variables are as follows:
#'
#' @format A data frame with 200 rows and 40 variables:
#' \describe{
#'   \item{gr_id}{Group id}
#'   \item{symbol}{Gene symbol}
#'   \item{accession_id}{Gene accession id (RefSeq)}
#'   \item{locus}{Genome locus}
#'   \item{CTRL_1_0h}{RPKM value at 0h in control condition}
#'   \item{CTRL_1_1h}{RPKM value at 1h in control condition}
#'   \item{CTRL_1_2h}{RPKM value at 2h in control condition}
#'   \item{CTRL_1_4h}{RPKM value at 4h in control condition}
#'   \item{CTRL_1_8h}{RPKM value at 8h in control condition}
#'   \item{CTRL_1_12h}{RPKM value at 12h in control condition}
#'   \item{gr_id}{Group id}
#'   \item{symbol}{Gene symbol}
#'   \item{accession_id}{Gene accession id (RefSeq)}
#'   \item{locus}{Genome locus}
#'   \item{CTRL_2_0h}{RPKM value at 0h in control condition}
#'   \item{CTRL_2_1h}{RPKM value at 1h in control condition}
#'   \item{CTRL_2_2h}{RPKM value at 2h in control condition}
#'   \item{CTRL_2_4h}{RPKM value at 4h in control condition}
#'   \item{CTRL_2_8h}{RPKM value at 8h in control condition}
#'   \item{CTRL_2_12h}{RPKM value at 12h in control condition}
#'   \item{gr_id}{Group id}
#'   \item{symbol}{Gene symbol}
#'   \item{accession_id}{Gene accession id (RefSeq)}
#'   \item{locus}{Genome locus}
#'   \item{CTRL_3_0h}{RPKM value at 0h in control condition}
#'   \item{CTRL_3_1h}{RPKM value at 1h in control condition}
#'   \item{CTRL_3_2h}{RPKM value at 2h in control condition}
#'   \item{CTRL_3_4h}{RPKM value at 4h in control condition}
#'   \item{CTRL_3_8h}{RPKM value at 8h in control condition}
#'   \item{CTRL_3_12h}{RPKM value at 12h in control condition}
#'   \item{gr_id}{Group id}
#'   \item{symbol}{Gene symbol}
#'   \item{accession_id}{Gene accession id (RefSeq)}
#'   \item{locus}{Genome locus}
#'   \item{KD_1_0h}{RPKM value at 0h in knockdown condition}
#'   \item{KD_1_1h}{RPKM value at 1h in knockdown condition}
#'   \item{KD_1_2h}{RPKM value at 2h in knockdown condition}
#'   \item{KD_1_4h}{RPKM value at 4h in knockdown condition}
#'   \item{KD_1_8h}{RPKM value at 8h in knockdown condition}
#'   \item{KD_1_12h}{RPKM value at 12h in knockdown condition}
#' }
"RNA_halflife_grubbs_test"


#' BRIC-seq result dataset for p-value estimation using grubbs test
#'
#' A dataset containing the RPKM for each time point, information column,
#' RNA half-life, R2 and fitting model about 200 genes.
#' The variables are as follows:
#'
#' @format A data frame with 200 rows and 52 variables:
#' \describe{
#'   \item{gr_id}{Group id}
#'   \item{symbol}{Gene symbol}
#'   \item{accession_id}{Gene accession id (RefSeq)}
#'   \item{locus}{Genome locus}
#'   \item{T00_1}{RPKM value at 0h in control condition}
#'   \item{T01_1}{RPKM value at 1h in control condition}
#'   \item{T02_1}{RPKM value at 2h in control condition}
#'   \item{T04_1}{RPKM value at 4h in control condition}
#'   \item{T08_1}{RPKM value at 8h in control condition}
#'   \item{T12_1}{RPKM value at 12h in control condition}
#'   \item{Model}{RNA decay fitting model}
#'   \item{R2}{R2 for fitting curve}
#'   \item{half_life}{RNA half-life}
#'   \item{gr_id}{Group id}
#'   \item{symbol}{Gene symbol}
#'   \item{accession_id}{Gene accession id (RefSeq)}
#'   \item{locus}{Genome locus}
#'   \item{T00_2}{RPKM value at 0h in control condition}
#'   \item{T01_2}{RPKM value at 1h in control condition}
#'   \item{T02_2}{RPKM value at 2h in control condition}
#'   \item{T04_2}{RPKM value at 4h in control condition}
#'   \item{T08_2}{RPKM value at 8h in control condition}
#'   \item{T12_2}{RPKM value at 12h in control condition}
#'   \item{Model}{RNA decay fitting model}
#'   \item{R2}{R2 for fitting curve}
#'   \item{half_life}{RNA half-life}
#'   \item{gr_id}{Group id}
#'   \item{symbol}{Gene symbol}
#'   \item{accession_id}{Gene accession id (RefSeq)}
#'   \item{locus}{Genome locus}
#'   \item{T00_3}{RPKM value at 0h in control condition}
#'   \item{T01_3}{RPKM value at 1h in control condition}
#'   \item{T02_3}{RPKM value at 2h in control condition}
#'   \item{T04_3}{RPKM value at 4h in control condition}
#'   \item{T08_3}{RPKM value at 8h in control condition}
#'   \item{T12_3}{RPKM value at 12h in control condition}
#'   \item{Model}{RNA decay fitting model}
#'   \item{R2}{R2 for fitting curve}
#'   \item{half_life}{RNA half-life}
#'   \item{gr_id}{Group id}
#'   \item{symbol}{Gene symbol}
#'   \item{accession_id}{Gene accession id (RefSeq)}
#'   \item{locus}{Genome locus}
#'   \item{T00_4}{RPKM value at 0h in knockdown condition}
#'   \item{T01_4}{RPKM value at 1h in knockdown condition}
#'   \item{T02_4}{RPKM value at 2h in knockdown condition}
#'   \item{T04_4}{RPKM value at 4h in knockdown condition}
#'   \item{T08_4}{RPKM value at 8h in knockdown condition}
#'   \item{T12_4}{RPKM value at 12h in knockdown condition}
#'   \item{Model}{RNA decay fitting model}
#'   \item{R2}{R2 for fitting curve}
#'   \item{half_life}{RNA half-life}
#' }
"halflife_table"