my.rowMeans doesnt work

[SergejRuff]

hello,

In music_S the my.rowMeans doesnt work. It returns teh same as

S <- sapply(unique(clusters), function(ct){
sapply(unique(samples), function(sid){
y = counts(x)[, clusters %in% ct & samples %in% sid]
if(is.null(dim(y))){
return(sum(y))
}else{
return(sum(y)/ncol(y))
}
})
})

instead of

S <- sapply(unique(clusters), function(ct){
my.rowMeans(sapply(unique(samples), function(sid){
y = counts(x)[, clusters %in% ct & samples %in% sid]
if(is.null(dim(y))){
return(sum(y))
}else{
return(sum(y)/ncol(y))
}
}), na.rm = TRUE)
})

is that on purpose or a mistake?

I utilized the single cell dataset from your vignete EMTABsce_healthy.rds.

lib_size <- music_S(x=EMTAB.sce, non.zero=TRUE, clusters='cellType', samples='sampleID',
select.ct=c('alpha', 'beta', 'delta', 'gamma',
'acinar', 'ductal'))

returns

  alpha     beta    delta     gamma    acinar    ductal

1 1112535.6 672700.3 771492.5 441998.45 1931490.1 745700.5
2 950452.0 843435.9 813057.3 656086.57 1082554.4 1065658.7
4 384778.1 362149.6 328635.8 320486.22 540339.3 443171.8
5 263706.3 328880.0 318821.2 270594.95 505857.6 354052.4
6 240645.2 137893.2 250652.9 87412.08 241888.4 371934.3
8 231126.2 139679.5 119419.0 506790.55 112532.5 192096.1

Whereas

EMTAB.sce = EMTAB.sce[, EMTAB.sce@colData[, 'cellType'] %in% c('alpha', 'beta', 'delta', 'gamma',
'acinar', 'ductal')]
x <- EMTAB.sce[rowSums(counts(EMTAB.sce))>0, ]
clusters <- as.character(colData(EMTAB.sce)[, 'cellType'])
samples <- as.character(colData(EMTAB.sce)[,'sampleID'])

S <- sapply(unique(clusters), function(ct){
sapply(unique(samples), function(sid){
y = counts(x)[, clusters %in% ct & samples %in% sid]
if(is.null(dim(y))){
return(sum(y))
}else{
return(sum(y)/ncol(y))
}
})
})

returns

 delta     alpha     gamma    ductal

1 771492.5 1112535.6 441998.45 745700.5
2 813057.3 950452.0 656086.57 1065658.7
4 328635.8 384778.1 320486.22 443171.8
5 318821.2 263706.3 270594.95 354052.4
6 250652.9 240645.2 87412.08 371934.3
8 119419.0 231126.2 506790.55 192096.1
acinar beta
1 1931490.1 672700.3
2 1082554.4 843435.9
4 540339.3 362149.6
5 505857.6 328880.0
6 241888.4 137893.2
8 112532.5 139679.5