How to get the proportion of cells accessible for a certain peak

[siyuyang1013]

Hello~
How to get the proportion of cells accessible for a certain peak, for example, chr1:800-1300 This peak has 100 cells accessible in the microglia, and the total number of cells in the microglia is 1000, then the proportion of accessible open for this peak is 100/1000

[Zepeng-Mu]

Isn't it the same as getting the peakMatrix and count how many cells have non-zero values for that given peak?

[siyuyang1013]

But when I extracted the peak matrix, I realized that this matrix has no row names, i.e. no peak names

peaks.mat
class: RangedSummarizedExperiment
dim: 447926 33409
metadata(0):
assays(1): PeakMatrix
rownames: NULL
rowData names(1): idx
colnames(33409): F#AAAGATGCAGGTCCTG-1 F#ACAGCGCTCGGGACAA-1 ...
M#CTCAACCAGTGAGTTA-1 M#GCGGAAAGTATCCCTC-1
colData names(25): DoubletEnrichment DoubletScore ... predictedGroup_Un
predictedScore_Un

[Zepeng-Mu]

So this is a more general question then, it's not just about counting non-zero values.
But the idx in rowData should match that of peakSet. You could also try rowRanges(peaks.mat), or use seqnames(peaks.mat), start(peaks.mat) and end(peaks.mat) to get the chr, start and end of each peak.

[siyuyang1013]

actually, the number of row in seqnames(peaks.mat) does not match the number of row in peaks.mat

[Zepeng-Mu]

it's hard to say why without looking at the output