geneloc

Artificial Gene location file for 10 genes.<table><tr><td>
 geneid </td>
<td> chr </td>
<td> left </td>
<td> right </td>
</tr><tr><td>
 Gene_01 </td>
<td> chr1 </td>
<td> 721289 </td>
<td> 731289 </td>
</tr><tr><td>
 Gene_02 </td>
<td> chr1 </td>
<td> 752565 </td>
<td> 762565 </td>
</tr><tr><td>
 &#8230; </td>
<td> &#8230; </td>
<td> &#8230; </td>
<td> &#8230; </td>
</tr></table>

datasets

Matrix eQTL is designed for fast eQTL analysis on large datasets.
Matrix eQTL can test for association between genotype
and gene expression using linear regression
with either additive or ANOVA genotype effects.
The models can include covariates to account for factors
as population stratification, gender, and clinical variables.
It also supports models with heteroscedastic and/or correlated errors,
false discovery rate estimation and
separate treatment of local (cis) and distant (trans) eQTLs.
For more details see Shabalin (2012) <doi:10.1093/bioinformatics/bts163>.

Andrey A Shabalin

MatrixEQTL

Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix
Operations

geneloc function

A data frame with 4 columns.<dl class="dl-horizontal">
 <dt><code>geneid</code></dt><dd>A column with gene names. 
 The order does not have to match the gene expression data set.</dd>
 <dt><code>chr</code></dt><dd>Chromosome number, i.e. chr1.</dd>
 <dt><code>left</code></dt><dd>Lower (smaller) coordinate of the gene begining/end.</dd>
 <dt><code>right</code></dt><dd>Upper (larger) coordinate of the gene begining/end.</dd>
 </dl>

Format

Artificial data for Matrix eQTL sample code: Gene location file. — geneloc

A data frame with 4 columns.<dl class='dl-horizontal'>
 <dt><code>geneid</code></dt><dd>A column with gene names. 
 The order does not have to match the gene expression data set.</dd>
 <dt><code>chr</code></dt><dd>Chromosome number, i.e. chr1.</dd>
 <dt><code>left</code></dt><dd>Lower (smaller) coordinate of the gene begining/end.</dd>
 <dt><code>right</code></dt><dd>Upper (larger) coordinate of the gene begining/end.</dd>
 </dl>

geneloc: Artificial data for Matrix eQTL sample code: Gene location file.

Description

Arguments

Format

References

See Also

geneid	chr	left	right
Gene_01	chr1	721289	731289
Gene_02	chr1	752565	762565
…	…	…	…