doc: add README

Author: js2264

README.md

@@ -0,0 +1,60 @@
+# tidyCoverage
+
+## Load libraries and example datasets
+
+```r
+library(tidyCoverage)
+library(tidySummarizedExperiment)
+library(rtracklayer)
+library(plyranges)
+library(purrr)
+library(ggplot2)
+
+# ~~~~~~~~~~~~~~~ Import genomic features into a named list ~~~~~~~~~~~~~~~ #
+features <- list(
+    TSSs = system.file("extdata", "TSSs.bed", package = "tidyCoverage"),
+    conv_sites = system.file("extdata", "conv_transcription_loci.bed", package = "tidyCoverage")
+) |> map(~ import(.x))
+
+# ~~~~~~~~~~~~ Import coverage tracks into a `BigWigFileList` ~~~~~~~~~~~~~ #
+tracks <- list(
+    Scc1 = system.file("extdata", "Scc1.bw", package = "tidyCoverage"), 
+    RNA_fwd = system.file("extdata", "RNA.fwd.bw", package = "tidyCoverage"),
+    RNA_rev = system.file("extdata", "RNA.rev.bw", package = "tidyCoverage"),
+    PolII = system.file("extdata", "PolII.bw", package = "tidyCoverage"), 
+    MNase = system.file("extdata", "MNase.bw", package = "tidyCoverage")
+) |> BigWigFileList()
+```
+
+## Plot tracks coverage aggregated over genomic features
+
+```r
+CoverageExperiment(tracks, features, width = 3000, ignore.strand = FALSE) |> 
+    filter(track %in% c('MNase', 'PolII')) |> 
+    filter(features == 'TSSs') |> 
+    aggregate() |> 
+    ggplot(aes(x = coord, y = mean)) + 
+    geom_ribbon(aes(ymin = ci_low, ymax = ci_high, fill = track), alpha = 0.2) + 
+    geom_line(aes(col = track)) + 
+    facet_grid(track ~ ., scales = "free") + 
+    labs(x = 'Distance from TSS', y = 'Signal coverage') + 
+    theme_bw() + 
+    theme(legend.position = 'top')
+```
+
+![](man/figures/aggr-cov.png)
+
+## Plot coverage over a single locus
+
+```r
+CoverageExperiment(tracks, GRanges("II:450001-455000"), width = 5000) |> 
+    expand() |> 
+    ggplot(aes(x = coord, y = coverage)) + 
+        geom_col(aes(fill = track, col = track)) + 
+        facet_grid(track~., scales = 'free') + 
+        scale_x_continuous(expand = c(0, 0)) + 
+        theme_bw() + 
+        theme(legend.position = "none", aspect.ratio = 0.1)
+```
+
+![](man/figures/cov.png)

man/figures/aggr-cov.png

@@ -327,3 +327,9 @@ AC |>
 ```
 
 ![](../man/figures/PTMs-TSSs.png)
+
+## Session info
+
+```{r}
+sessionInfo()
+```