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count_table.R
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count_table.R
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#' Table of the count table
#' @docType data
#' @usage data(count_table)
#' @keywords datasets
#' @concept data
#'
#' @format A data frame with 5323 rows and 15 variables obtained from
#' barcode alignment to the reference library.
#' It is generated from a [Cellecta](https://cellecta.com/) protocol.
#' The samples generated are then sequenced using an RNA-seq protocol.
#' Due to the fact that different shRNAs are sequenced for a gene each
#' barcode has its associated reads. This reads were aligned to the
#' reference library using [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
#' and then sorted with [samtools](https://github.com/samtools/samtools).
#' Since this dataset comes from a Chemical Synthetic Lethality
#' experiments the samples treated and combined with the shRNAs
#' knockdown should present a decreased number of reads compared to
#' the controls.
#'
#' \describe{
#' \item{Barcode}{It contains an ID that identify each barcode. It can be use
#' to marge the annotation table with the count table. A Barcode is a unique
#' identifier of an shRNA. In a genetic screening multiple slightly different
#' shRNAs perform a knockout of a gene each with its efficacy. For this reason
#' it is important to keep track of each shRNA using a unique barcode.}
#'
#' \item{Time_1}{It contains the counts at time zero.
#' This is the first time point at which cells are not treated
#' and not infected.}
#'
#' \item{Time_2}{It contains the counts after the cell were washed.
#' At this time point the cells are infected and following the
#' Cellecta protocol are washed with the puromycin.}
#'
#' \item{Time_3_TRT_rep1}{It contains the counts for the first replicate
#' of the treated at the first time point.
#' Usually the first time point is 7 day after the puromycin
#' wash.}
#'
#' \item{Time_3_TRT_rep2}{It contains the counts for the second replicate
#' of the treated at the first time point. Usually the first
#' time point is 7 day after the puromycin wash.}
#'
#' \item{Time_3_TRT_rep3}{It contains the counts for the third replicate
#' of the treated at the first time point. Usually the first
#' time point is 7 day after the puromycin wash.}
#'
#' \item{Time_3_rep1}{It contains the counts for the first replicate of the
#' control at the first time point. Usually the first
#' time point is 7 day after the puromycin wash.}
#'
#' \item{Time_3_rep2}{It contains the counts for the second replicate of the
#' control at the first time point. Usually the first
#' time point is 7 day after the puromycin wash.}
#'
#' \item{Time_3_rep3}{It contains the counts for the third replicate of the
#' control at the first time point. Usually the first
#' time point is 7 day after the puromycin wash.}
#'
#' \item{Time_4_TRT_rep1}{It contains the counts for the first replicate
#' of the treated at the second time point. Usually the first
#' time point is 14 day after the puromycin wash.}
#'
#' \item{Time_4_TRT_rep2}{It contains the counts for the second replicate
#' of the treated at the second time point. Usually the first
#' time point is 14 day after the puromycin wash.}
#'
#' \item{Time_4_TRT_rep3}{It contains the counts for the third replicate
#' of the treated at the second time point. Usually the first
#' time point is 14 day after the puromycin wash.}
#'
#' \item{Time_4_rep1}{It contains the counts for the first replicate of the
#' control at the second time point. Usually the first
#' time point is 14 day after the puromycin wash.}
#'
#' \item{Time_4_rep2}{It contains the counts for the second replicate of the
#' control at the second time point. Usually the first
#' time point is 14 day after the puromycin wash.}
#'
#' \item{Time_4_rep3}{It contains the counts for the third replicate of the
#' control at the second time point. Usually the first
#' time point is 14 day after the puromycin wash.}
#' }
#'
"count_table"