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

%\VignetteEngine{knitr::knitr} %\VignetteIndexEntry{AnimalGene2QTL}

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.

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.listQTLfunction 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,listSNPattributesfunction display it.

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:

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"

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"

snp <- getSNPbyQTL('refsnp_id','QTL_ID','4097',2);
head(snp)

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