Fixed to ensure that all the genes in the peak.info.list file are in …

…RNA matrix
immunogenomics · Aug 9, 2024 · 75071bd · 75071bd
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diff --git a/R/SCENTfunctions.R b/R/SCENTfunctions.R
@@ -252,6 +252,8 @@ CreatePeakToGeneList <- function(object,genebed="/path/to/GeneBody_500kb_margin.
   #Obtain gene to peak pairs.
   cis.g2p <- d[c("V4","V8")]
   colnames(cis.g2p) <- c("gene","peak")
+  genes_in_rna <- rownames(object@rna) # gene by cell matrix
+  cis.g2p <- cis.g2p[cis.g2p$gene %in% genes_in_rna,] # make sure g2p genes are all included in rna matrix
 
   cis.g2p$index <- 1:nrow(cis.g2p)
   cis.g2p$batch_index <- cut2(cis.g2p$index, g = nbatch, levels.mean = TRUE)

diff --git a/README.md b/README.md
@@ -4,8 +4,6 @@
 
 Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA
 
-(*beta version*)
-
 The manuscript is now publised in *Nature Genetics*! (Sakaue et al. ["**Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles**"](https://www.nature.com/articles/s41588-024-01682-1))
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Expand Up		@@ -4,8 +4,6 @@

		Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA

		(beta version)

		The manuscript is now publised in Nature Genetics! (Sakaue et al. ["Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles"](https://www.nature.com/articles/s41588-024-01682-1))


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