Write a template script that fetches probe coordinates from Bioconductor

The heavyweight route, kept for people who already have the annotation packages installed. dmsa_probe_coords does the same job from a plain-text manifest with base R only, and dmsa_plot_locus needs no coordinates at all.

Usage

dmsa_probe_annotation_template(
  path = "get_probe_coords.R",
  array = c("EPIC", "450K")
)

Arguments

path

Where to write the script.

array

"EPIC" or "450K".

Value

path, invisibly.

Details

Run the written script once; it produces a csv with probe, chr, pos, gene_region, island that dmsa_plot_locus() consumes.

See also

dmsa_probe_coords

Examples

f <- tempfile(fileext = ".R")
dmsa_probe_annotation_template(f, array = "EPIC")
#> wrote /var/folders/yd/5vhpvlls31x18db51sk7y_zh0000gn/T//RtmpUh53Rl/file766433461c24.R - run it once, then join probe_coords.csv to your probes. Lighter: dmsa_probe_coords(), or skip coordinates entirely.
## the script is not run here: it installs and queries the minfi annotation
## packages. dmsa_probe_coords() does the same job from a plain manifest.
head(readLines(f), 5)
#> [1] "# Probe coordinates for dmsa_plot_locus(). Run once."                                 
#> [2] "# Lighter alternatives: dmsa_probe_coords(), or no coordinates at all."               
#> [3] "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager')"
#> [4] "BiocManager::install(c('minfi', 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19'))"    
#> [5] "library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19); library(minfi)"