CNA integer states on UMAP

[RaghadShu]

Hello,
Thank you very much for developing this great tool!

I am estimating CNAs in one sample, and would like to plot the CNA state (0,1,2,3 or 4) of each cell in the 1q arm of the chromosome. More specifically, I want to look at this region (1q21.3) or the genes affected from this reigon (in this case they are PYGO2, CKS1B and ZBTB7B).

I would like to have a Seurat UMAP that shows the score (0-4) of each cell in this specific reigon. You mentioned in #80 that integer copy number for all positions is found in the .seg files. But I am very confused on how to connect this information to my single-cell barcodes and subsequently map them into the UMAP.
Is this something we can do with SCEVAN? and if so, I would really appreciate your guidance on how to do this.

Best,
Raghad

[AntonioDeFalco]

Hi @RaghadShu.
Integer copy number inference in SCEVAN is performed at the clonal or subclonal level, if you want to plot the copy number information at the single cell level you can use the log-ratio in the CNA matrix. In the seg file you can get the region of the alteration you are interested in and you can plot then at single cell level e.g. like this:

`
load(url("https://www.dropbox.com/s/b9udpvhnc2ez9pc/MGH106_data.RData?raw=1"))

seur_obj <- Seurat::CreateSeuratObject(count_mtx)
seur_obj <- NormalizeData(seur_obj)
all.genes <- rownames(seur_obj)
seur_obj <- ScaleData(seur_obj, features = all.genes)
seur_obj <- FindVariableFeatures(seur_obj)
seur_obj <- RunPCA(seur_obj, features = VariableFeatures(object = seur_obj))
seur_obj <- RunUMAP(seur_obj, dims = 1:10)

load("output/MGH106_count_mtx_annot.RData")
load("output/MGH106_CNAmtx.RData")

chr3 <- apply(CNA_mtx_relat[count_mtx_annot$seqnames==3 & count_mtx_annot$start>=158644278 & count_mtx_annot$end<=194498364,], 2, mean)
chr3 <- chr3[rownames(seur_obj@meta.data)]
names(chr3) <- rownames(seur_obj@meta.data)
chr3 <- as.data.frame(chr3)

seur_obj <- AddMetaData(seur_obj, metadata = chr3)
Seurat::FeaturePlot(seur_obj, "chr3", cols = c("gray", "red"))
`

I hope I was clear and that this was what you wanted.

Let me know, regards.