06_probe_id_conversion.Rmd

# Probe ID conversion {#probe-id-conversion-1}

```{r include=FALSE}
library(knitr)
opts_chunk$set(message = FALSE, warning = FALSE, eval = TRUE, echo = TRUE, cache = TRUE)
library(genekitr)
library(dplyr)
```

Probes are used to measure the expression level of many genes. After getting micro array data, the first important thing before downstream analysis maybe probe id conversion.

Ensembl database regularly maps probes sets against the latest set of transcript models using their own [pipeline]((https://www.ensembl.org/info/genome/microarray_probe_set_mapping.html)).

Here, `transProbe` utilizes Ensembl up-to-date annotation datasets and could join together with other genekitr functions fluently.

> Notice: now we only support human data

## Supported platforms {#transProbe-supported-platforms}

36 probe platforms include Affymetrix, Agilent, Illumina, Codelink and Phalanx.

```{r}
DT::datatable(hsapiens_probe_platform, options = list(pageLength = 10))
```

## Basic usage {#probe-basic-usage}

`transProbe` has four arguments:

- `id`: probe id
- `transTo`: the conversion target type. User could select **more than one** from "symbol", "entrez", "ensembl" or "uniprot".
- `org`: human (default)
- `platform`: Probe platform. If not given, program will detect automatically.


```{r}
data(deg, package = "genekitr")
probes <- deg$probe_id

res <- transProbe(probes, transTo = "ensembl", org = "human")
head(probes)
head(res)
```


## Convert to more than one type {#convert-probe-types}

User could define `transTo` as many types:

```{r}
res2 <- transProbe(probes, transTo = c("ensembl","symbol"), org = "human")
head(res2)
```

Let's take the first record as example:`r Ensembl("ENSG00000228794")` has 38 transcripts. 

When we look at its second transcript [ENST00000445118.7](http://asia.ensembl.org/Homo_sapiens/Transcript/Oligos?db=core;g=ENSG00000228794;r=1:825138-859446;t=ENST00000445118), probe `7896759` is listed in `AFFY HuGene-1_0-st-v1` database.