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### summary statistics for dealing with duplicated gene names in exprssion matrix | ||
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#' @title Aggregate duplicate gene rows | ||
#' @description Aggregate duplicate gene rows. Duplicate rows are collapsed into one by taking the colSums, colMeans, colMaxs or colMedians. | ||
#' @param m matrix with genes as rows | ||
#' @param stat statistic to aggregate duplicate gene rows. Defaults to 'sum'. Default: c("sum", "mean", "max", "median") | ||
#' @return matrix with unique gene rows | ||
#' @seealso | ||
#' \code{\link[matrixStats]{rowSums2}},\code{\link[matrixStats]{rowMeans2}},\code{\link[matrixStats]{rowRanges}},\code{\link[matrixStats]{rowMedians}} | ||
#' @rdname aggr_dup_genes | ||
#' @export | ||
#' @importFrom matrixStats colSums2 colMeans2 colMaxs colMedians | ||
aggr_dup_genes = function(m, stat=c('sum','mean','max','median'), na.rm=T) { | ||
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aggr_dup_gene = function(gene) { | ||
mgene = m[rownames(m)==gene,] | ||
statFUN(mgene, na.rm=na.rm) | ||
} | ||
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statFUN = switch(match.arg(stat), | ||
sum = matrixStats::colSums2, | ||
mean = matrixStats::colMeans2, | ||
max = matrixStats::colMaxs, | ||
median = matrixStats::colMedians) | ||
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one_col=FALSE | ||
if (ncol(m)==1) { | ||
one_col=TRUE | ||
m = cbind(m, m) | ||
} | ||
# gene order, keeping only first instance of dup.genes | ||
gene.ord = rownames(m)[!duplicated(rownames(m))] | ||
# find dup genes | ||
dup.genes = unique(rownames(m)[duplicated(rownames(m))]) | ||
# for each dup genes, apply summary statistic and return numeric vec | ||
# rbind dup gene vectors | ||
mNew = do.call(rbind, sapply(dup.genes, aggr_dup_gene, simplify = F)) | ||
m = m[!rownames(m) %in% dup.genes, ] | ||
m = rbind(m, mNew) | ||
#m = m[gene.ord,] | ||
if(one_col) { | ||
m = m[,1,drop=F] | ||
} | ||
m | ||
} |