Commit 2315be90 authored by domingue's avatar domingue

Fixed issue related to missing gene names in more standard gtf annotations....

Fixed issue related to missing gene names in more standard gtf annotations. Tested with Homo sapiens (Ensembl_v88_custom, GRCh38).
parent 294dc4fd
......@@ -701,6 +701,16 @@ rowRanges(dds) <- exons
attr <- c("ensembl_gene_id", "external_gene_name", "description", "chromosome_name", "start_position", "end_position")
if (exists("gtf")) {
geneDescs <- gtf %>%
as.data.frame() %>%
rename_all(recode,
gene_id = "ensembl_gene_id",
gene_name = "external_gene_name",
gene_description = "description"
) %>%
select(one_of(c("ensembl_gene_id", "external_gene_name", "description"))) %>%
distinct()
geneInfo <- genes %>%
as.data.frame() %>%
rename_all(recode,
......@@ -710,7 +720,8 @@ if (exists("gtf")) {
start = "start_position",
end = "end_position"
) %>%
dplyr::select(one_of(attr))
select(one_of(c("ensembl_gene_id", "chromosome_name", "start_position", "end_position"))) %>%
left_join(geneDescs)
} else if (is.null(gene_info_file)) {
## optionally install bioconducor package
......
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