README.md

In liuyufong/AnimalGene2QTL: Get the QTL/gene/SNP data functions

Introduction

The AnimalGene2QTL provides an interface to retrieve QTL data , gene data , SNP data.The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries.

Quick start

Viewing AnimalGene2QTL dataset

Every analysis with AnimalGene2QTL starts with Viewing a AnimalGene2QTL dataset to use. The function listQTL will display all available QTL dataset.

```{r eval=TRUE} library(AnimalGene2QTL) listQTL()

## `How to build a QTL query`
The `getAnimalQTL` function has six arguments that need to be
introduced:
*gene_filters*, *qtl_attributes*, *gene_values*, *data_set*
, *snp*, *snp_attributes*.

* **gene_filters**: define a restriction on the query.
For example you want to restrict the output to all QTL located
on the human X chromosome
then the `gene_filters`:`chromosome_name` can be used with gene
values `X`.
The `listGeneAF` function displays all available gene filters
in the selected dataset.
* **qtl_attributes**: define the values we are interested in to retrieve.
For example we want to retrieve the QTL ID or QTL name.
The `listQTLAF` function displays all available QTL attributes
in the selected dataset.
* **gene_values**: The input gene data.
* **data_set**: There are five numbers:1,2,3,4,5.`listQTL`function display
which to input.
* **snp**: default FALSE,when it is TRUE,that mean retrieve SNP.
* **snp_attributes**: input the attribute of SNP what to retrieve,`listSNPattributes`function display it.
```{r eval=TRUE}
attributes <- listQTLAF()
head(attributes)
filters <- listGeneAF(1)
head(filters)

getAnimalQTL() function

The getAnimalQTL function is the main query function in AnimalGene2QTL. It has four main arguments.

• qtl_attributes: is a vector of attributes that one wants to retrieve (= the output of the query).
• gene_filters: is a vector of filter that one wil use as input to the query.
• gene_values: a vector of values for the gene_filters. In case multple filter are in use, the gene_values argument requires a list of values where each position in the list corresponds to the position of the filters in the gene_filters argument (see examples below).
• data_set: choose which animal QTL you want to retrieve.

Now that we selected a AnimalGene2QTL dataset, and know about qtl_attributes, gene_filters, and the gene_values for gene_filters; we can build a AnimalGene2QTL query. Let us make an easy query for the following problem: We have a list of gene identifiers from the Ensembl and we want to retrieve the QTL identifiers. Let us now run the query:

```{r eval=TRUE} geneid <- c("ENSBTAG00000009851", "ENSBTAG00000005101", "ENSBTAG00000036262") qtl <- getAnimalQTL(qtl_attributes=c('QTL_ID'),gene_filters='ensembl_gene_id' ,gene_values=geneid,data_set=1); head(qtl);

## `Examples of AnimalGene2QTL queries`
In the sections below a variety of example
queries are described.
Every example is written
as a task, and we have to come up with a `AnimalGene2QTL`
solution to the problem.

### `Task 1: Retrieve all identifiers of genes by QTL`
`identifiers:"64577","2199","2354"`

```{r eval=TRUE}
qtlid <- c("64577","2199","2354");
gene <- getAnimalGene(gene_attributes="ensembl_gene_id",qtl_filters=c("QTL_ID")
,qtl_values=qtlid, data_set=2);
head(gene)

Task 2: Retrieve all identifiers of SNP by QTL

identifiers:"4097"

{r eval=TRUE} snp <- getSNPbyQTL('refsnp_id','QTL_ID','4097',2); head(snp)

liuyufong/AnimalGene2QTL documentation built on May 9, 2019, 12:48 p.m.