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Add pseudo_count to log2_FC so zero mean genes don't break fold changes #9

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Add pseudo_count to log2_FC so zero mean genes don't break fold changes #9

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14 changes: 9 additions & 5 deletions R/log2_FC.R
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
#' indicating the name of the colData(x) element which stores the group id of each cell (i.e., colData(x)$name_group).
#' @param name_cluster a character ("cluster_id" by default),
#' indicating the name of the colData(x) element which stores the cluster id of each cell (i.e., colData(x)$name_cluster).
#' @param pseudo_count average count to be added to each observation to avoid taking log of zero when computing FCs. Default is 0 (backward compatible).
#' @return A \code{\linkS4class{data.frame}} object, extending the results in `res`.
#' Two additional columns are added: FC_group1/group2 and log2FC_group1/group2, inicating the FC and log2-FC of group1/group2.
#' A FC > 1 (or log2FC > 0) indicates up-regulation of group1 (compared to group2); while a FC < 1 (or log2FC < 0) indicates down-regulation of group1 (compared to group2).
Expand All @@ -36,18 +37,20 @@
#' @seealso \code{\link{distinct_test}}, \code{\link{top_results}}
#'
#' @export
log2_FC = function(res,
x,
log2_FC = function(res,
x,
name_assays_expression = "cpm",
name_group = "group_id",
name_cluster = "cluster_id"
name_cluster = "cluster_id",
pseudo_count = 0
){
stopifnot(
is.data.frame(res),
( is(x, "SummarizedExperiment") | is(x, "SingleCellExperiment") ),
is.character(name_assays_expression), length(name_assays_expression) == 1L,
is.character(name_group), length(name_group) == 1L,
is.character(name_cluster), length(name_cluster) == 1L
is.character(name_cluster), length(name_cluster) == 1L,
is.numeric(pseudo_count), length(pseudo_count) == 1L, pseudo_count >= 0
)

# check if FC/log2_FC are already present in res:
Expand Down Expand Up @@ -127,7 +130,8 @@ log2_FC = function(res,
FC_by_cluster = lapply(seq_along(cluster_levels), function(i){
exp_1 = pb_1[,i]
exp_2 = pb_2[,i]
FC = exp_1/exp_2
# add pseudo_count to avoid division by zero when computing FCs
FC = (exp_1 + pseudo_count)/(exp_2 + pseudo_count)
log2_FC = log2(FC)

cbind( cluster_num = i, gene_num = seq_len(n_genes), exp_1, exp_2, FC, log2_FC)
Expand Down