These functions are in response to StackOverflow questions like [this][], wanting to fill in missing NA values with preceeding values, optionally by group
fill_down <- function(v) {
if (length(v) > 1) {
keep <- c(TRUE, !is.na(v[-1]))
v[keep][cumsum(keep)]
} else v
| suppressPackageStartupMessages({ | |
| library(tibble) | |
| library(GenomicRanges) | |
| }) | |
| .g_range <- setClass("g_range", contains="GRanges") | |
| .g_columns <- c("chr", "start", "end", "strand") | |
| setAs("GRanges", "g_range", function(from) { |
| dna <- getFastaSeq() | |
| ## function for finding orfs. Returned as IRanges. | |
| ORFdef <- find_in_frame_ORFs(dna, longestORF = FALSE, minimumLength = 8) | |
| ORFdef <- ORFdef[lengths(ORFdef) > 0] | |
| ## Map (mapply) on each five prime leader | |
| uORFs <- Map( | |
| function(granges, tx_name, ORFdef) { | |
| map_granges(ORFdef, granges, tx_name) | |
| }, |
| .host <- "localhost" | |
| .port <- 5001 | |
| library(httr) | |
| library(BiocParallel) | |
| .get <- | |
| function(fmt, ..., host = .host, port = .port) | |
| { | |
| query <- sprintf(fmt, host, port, ...) |
| <!DOCTYPE html> | |
| <html lang="en"> | |
| <head> | |
| <script src="//cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script> | |
| <script src="//netdna.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script> | |
| <script src="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.11.0/highlight.min.js"></script> | |
| <script src="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.11.0/languages/r.min.js"></script> | |
| <link rel="stylesheet" type="text/css" href="/static/lib/prism/prism.css"> |
| ## package biocViews dumbbell | |
| library(BiocPkgTools) | |
| library(dplyr) | |
| library(tidyr) | |
| library(graph) | |
| library(biocViews) | |
| data(biocViewsVocab) |
| export BIOCVERSION_REPOS=~/b/git/BiocVersion | |
| export BIOCMANAGER_REPOS=~/b/git/BiocManager | |
| export BIOCMANAGER_SANDBOX=/Users/ma38727/tmp/BiocManagerSandbox | |
| # | |
| # R-4.0 | |
| # | |
| echo "R-4.0" | |
| export R_LIBS_USER=$BIOCMANAGER_SANDBOX/R-4.0-Bioc-3.10 |
| library(yaml) | |
| library(dplyr) | |
| library(tibble) | |
| library(lubridate) | |
| library(readr) | |
| library(memoise) | |
| get_releases <- | |
| function() | |
| { |
| obo = readLines("go.obo") | |
| ## | |
| ## Clean data | |
| ## | |
| ## blank lines separate different 'groups' in the obo | |
| group <- cumsum(!nzchar(obo)) | |
| ## keep groups that have the [Term] label |