R/params.R

In steinbaugh/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

#' @name params
#' @inherit AcidRoxygen::params return title
#' @keywords internal
#'
#' @param DESeqDataSet `DESeqDataSet` or `NULL`.
#'
#' @param DESeqTransform `DESeqTransform`.
#'
#' @param contrast `character`.
#' A character vector with exactly 3 elements:
#'
#' 1. Name of factor in the design formula.
#' 2. Name of numerator level for the fold change.
#' 3. Name of denominator level for the fold change.
#'
#' See `DESeq2::results()` for details.
#'
#' @param contrastSamples `logical(1)`.
#' Only include the samples used to define the contrast passed to
#' `DESeq2::results()`. This setting will break for complex DESeq2 contrasts
#' (e.g. interaction effect).
#'
#' @param i `character(1)` or `integer(1)`.
#' `DESeqResults` contrast name or position in `results` slot.
#'
#' @param lfcShrink `logical(1)` or `NULL`.
#' Use shrunken log2 fold change (LFC) values.
#' If `NULL`, inherits value defined in `lfcShrink()`.
#'
#' @param limits `list(2)`.
#' Named list containing `"x"` and `"y"` that define the lower and upper
#' limits for each axis. Set automatically by default when left `NULL`.
#'
#' @param name `character(1)`.
#' Name of the individual effect (coefficient) for building a results table.
#' Use this argument rather than `contrast` for continuous variables.
#'
#' @param results `character(1)` or `integer(1)`.
#' Name or position of `DESeqResults`.
NULL