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JasonJWilliamsNY merged 1 commit into from
Dec 15, 2025
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Add links to descriptions of VCF; resolves #281 #326

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7 changes: 7 additions & 0 deletions episodes/03-basics-factors-dataframes.Rmd
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of 29 variables (columns). Double-clicking on the name of the object will open
a view of the data in a new tab.

![RStudio data frame view](fig/rstudio_dataframeview.png)

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 [image missing alt-text]: fig/rstudio_dataframeview.png

The majority of the columns in the data frame correspond to standard fields found in a
*Variant Call Format (VCF)* file, while others were added during our data processing. The VCF
format is a standard format for storing variant calls (also known as Single Nucleotide Polymorphisms or SNPs),
and you can read more about it, including a description of the fields we have here
in [the VCF specification](https://samtools.github.io/hts-specs/VCFv4.2.pdf)
or [on wikipedia](https://en.wikipedia.org/wiki/Variant_Call_Format).

We can also quickly query the dimensions of the variable using `dim()`. You'll see that the first number `801` shows the number of rows, then `29` the number of columns

```{r, purl=FALSE}
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choose **From Excel...** (notice there are several other options you can
explore).

![RStudio import menu](fig/rstudio_import_menu.png)

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 [image missing alt-text]: fig/rstudio_import_menu.png

Next, under **File/Url:** click the <KBD>Browse</KBD> button and navigate to the **Ecoli\_metadata.xlsx** file located at `/home/dcuser/dc_sample_data/R`.
You should now see a preview of the data to be imported:

![RStudio import screen](fig/rstudio_import_screen.png)

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 [image missing alt-text]: fig/rstudio_import_screen.png

Notice that you have the option to change the data type of each variable by
clicking arrow (drop-down menu) next to each column title. Under **Import
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