From e0fb38998fa59d191cbfe1dd76e1e5fe161338cf Mon Sep 17 00:00:00 2001 From: LTLA Date: Mon, 9 Dec 2024 20:23:33 -0800 Subject: [PATCH] Cleaned up documentation for emptyDropsCellRanger. --- R/emptyDropsCellRanger.R | 8 +++++--- man/emptyDropsCellRanger.Rd | 8 +++++--- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/R/emptyDropsCellRanger.R b/R/emptyDropsCellRanger.R index 32d171b..8ec4df5 100644 --- a/R/emptyDropsCellRanger.R +++ b/R/emptyDropsCellRanger.R @@ -37,7 +37,8 @@ #' \item The first subset contains barcodes that are selected by the \dQuote{simple filtering algorithm}, which are regarded as high quality cells without any further filtering. #' The minimum threshold \eqn{T} for this subset is defined by taking the \code{max.percentile} percentile of the top \code{n.expected.cells} barcodes, #' and then dividing by the \code{max.min.ratio} to obtain a minimum UMI count. -#' All barcodes here will have an FDR of zero. +#' (This is closely related to the algorithm used by \code{\link{defaultDrops}}.) +#' All barcodes identified in this manner will have an FDR of zero. #' \item The second subset contains the ambient pool and is defined as all barcodes with rankings between \code{ind.min} and \code{ind.max}. #' The barcodes that fall in this category will be used to compute the ambient profile. #' None of these barcodes are considered to be potential cells. @@ -51,10 +52,11 @@ #' #' The main differences between \code{emptyDropsCellRanger} and \code{emptyDrops} are: #' \itemize{ -#' \item \code{emptyDropsCellRanger} applies a simple filtering strategy to identify some real cells before any further investigation. +#' \item \code{emptyDropsCellRanger} does not use the knee point to identify \dQuote{presumed real} cells, +#' instead relying on a threshold based on the expected number of cells. #' \item \code{emptyDropsCellRanger} takes barcodes whose total count ranks within a certain range - by default, \eqn{(45,000, 90,000]} - to compute the ambient profile. #' In contrast, \code{emptyDrops} only defines the upper bound using \code{lower} or \code{by.rank}. -#' \item \code{emptyDropsCellRanger} defines a cell candidate pool according to three parameters, \code{umi.min},\code{umi.min.frac.median} and \code{cand.max.n}. +#' \item \code{emptyDropsCellRanger} defines a cell candidate pool according to three parameters, \code{umi.min}, \code{umi.min.frac.median} and \code{cand.max.n}. #' In \code{emptyDrops}, this is only defined by \code{lower}. #' } #' diff --git a/man/emptyDropsCellRanger.Rd b/man/emptyDropsCellRanger.Rd index ae845e8..0bf6590 100644 --- a/man/emptyDropsCellRanger.Rd +++ b/man/emptyDropsCellRanger.Rd @@ -80,7 +80,8 @@ which itself was reverse-engineered from the behavior of CellRanger 3. \item The first subset contains barcodes that are selected by the \dQuote{simple filtering algorithm}, which are regarded as high quality cells without any further filtering. The minimum threshold \eqn{T} for this subset is defined by taking the \code{max.percentile} percentile of the top \code{n.expected.cells} barcodes, and then dividing by the \code{max.min.ratio} to obtain a minimum UMI count. -All barcodes here will have an FDR of zero. +(This is closely related to the algorithm used by \code{\link{defaultDrops}}.) +All barcodes identified in this manner will have an FDR of zero. \item The second subset contains the ambient pool and is defined as all barcodes with rankings between \code{ind.min} and \code{ind.max}. The barcodes that fall in this category will be used to compute the ambient profile. None of these barcodes are considered to be potential cells. @@ -94,10 +95,11 @@ All parameter defaults are set as the same as those used in STARsolo 2.7.9a. The main differences between \code{emptyDropsCellRanger} and \code{emptyDrops} are: \itemize{ -\item \code{emptyDropsCellRanger} applies a simple filtering strategy to identify some real cells before any further investigation. +\item \code{emptyDropsCellRanger} does not use the knee point to identify \dQuote{presumed real} cells, +instead relying on a threshold based on the expected number of cells. \item \code{emptyDropsCellRanger} takes barcodes whose total count ranks within a certain range - by default, \eqn{(45,000, 90,000]} - to compute the ambient profile. In contrast, \code{emptyDrops} only defines the upper bound using \code{lower} or \code{by.rank}. -\item \code{emptyDropsCellRanger} defines a cell candidate pool according to three parameters, \code{umi.min},\code{umi.min.frac.median} and \code{cand.max.n}. +\item \code{emptyDropsCellRanger} defines a cell candidate pool according to three parameters, \code{umi.min}, \code{umi.min.frac.median} and \code{cand.max.n}. In \code{emptyDrops}, this is only defined by \code{lower}. } }