Parameters in header

If you look at the de_template.Rmd, there is a section with options that will change what file and options to use to run the DE analysis:

params:
    se_file: "data/se.rds"
    design: "~ type + condition"
    contrast: "condition.treated_vs_untreated,type.paired-end_vs_single-read"
    metadata: !r c("condition", "type") # first one used in some plots
    alpha: 0.05
    lfc: 0
    slot: "vst"
    output_dir: "."
    cache_dir: "../cache"
    cache_on: FALSE

Let’s test this code. For that, we create a test folder.

R> dir.create("test", showWarnings = FALSE)

These are the ones by default that works with a test data, if we try to run this with these options, it will fail:

R> rmarkdown::render("de_template.Rmd", output_file = "test/de.html")

To have it working with our data, we need to change the options to match our data:

R> rmarkdown::render("de_template.Rmd",
+                   output_file = "test/de.html",
+                   quiet = TRUE,
+                   params = list(
+                       se_file = "data/gse.rds",
+                       design = "~ group",
+                       contrast = "group.E_vs_D",
+                       metadata = c("group"),
+                       output_dir = "test"
+                       
+                   )
+ )

## 00.05

Look at test/de.html.

Source

This template is available at PILM public GitHub. You can download from there the Rmd file.

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These materials have been developed by members of the teaching team at the PILM - MIT Bioinformatics Core (PILMBC). These are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.