---
title: "Download and Parse Seires matrix File from GEO database"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Download and Parse Seires matrix File from GEO database}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r setup}
library(geokit)
```

In many typical analysis workflows, a series matrix file is commonly used. You
can easily handle it in `geokit` using the `gse_matrix()` function. The
`gse_matrix()` function returns an `ExpressionSet` object, which is compatible
with many Bioconductor packages.

```{r gse_matrix, cache = TRUE}
gse_matix <- geo_matrix("GSE180383", odir = tempdir())
gse_matix
```

When parsing `phenoData` from series matrix files, the `gse_matrix()` function
automatically discerns `characteristics_ch*` columns and parses multiple traits
from them. Each trait is named with the prefix `ch*`, corresponding to the
column name.

```{r}
Biobase::pData(gse_matix)[c("ch1_cultivar", "ch1_genotypes")]
```

By default, `gse_matrix()` attempts to map the GPL accession to a Bioconductor annotation package. You can control this behavior using the `add_gpl` parameter:

* Set `add_gpl = FALSE` to exclude feature information.
* Set `add_gpl = TRUE` to include platform information from GEO.

```{r}
Biobase::annotation(gse_matix)
```

## Session Information
```{r}
sessionInfo()
```