update

Author: junjunlab

R/exporting-data.R

@@ -144,7 +144,7 @@ setMethod("export_genome_occupancy",
               # to GRanges
               adjusted <- adjusted %>%
                 fastplyr::f_group_by(sample,rname,pos) %>%
-                fastplyr::f_summarise(count = sum(count),rpm = sum(rpm), .groups = "drop") %>%
+                fastplyr::f_summarise(count = sum(count),rpm = sum(rpm)) %>%
                 fastplyr::f_select(rname,pos,rpm) %>%
                 dplyr::rename(seqnames = rname, start = pos,score = rpm) %>%
                 dplyr::mutate(end = start,.after = "start") %>%

R/generic-methods.R

@@ -55,6 +55,7 @@ setMethod("generate_summary",
                    exp_type = c("ribo", "rna", "total", "ip"),
                    load_local = FALSE,
                    nThreads = 1){
+            options(fastplyr.inform = FALSE)
             # exp_type <- match.arg(exp_type, c("ribo", "rna", "total", "ip"))
 
             bams <- subset(object@library, type %in% exp_type)