snpsloc

Artificial SNP location file for 15 markers.<table><tr><td>
 snpid </td>
<td> chr </td>
<td> pos </td>
<td>
 Snp_01 </td>
</tr><tr><td> chr1 </td>
<td> 721289 </td>
<td>
 Snp_02 </td>
<td> chr1 </td>
</tr><tr><td> 752565 </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

snpsloc function

A data frame with 3 columns.<dl class="dl-horizontal">
 <dt><code>snpid</code></dt><dd>A column with SNP names. 
 The order does not have to match the genotype data set.</dd>
 <dt><code>chr</code></dt><dd>Chromosome number, i.e. chr1.</dd>
 <dt><code>pos</code></dt><dd>Coordinate of the SNP.</dd>
 </dl>

Format

Artificial data for Matrix eQTL sample code: SNP location file. — snpsloc

A data frame with 3 columns.<dl class='dl-horizontal'>
 <dt><code>snpid</code></dt><dd>A column with SNP names. 
 The order does not have to match the genotype data set.</dd>
 <dt><code>chr</code></dt><dd>Chromosome number, i.e. chr1.</dd>
 <dt><code>pos</code></dt><dd>Coordinate of the SNP.</dd>
 </dl>

snpsloc: Artificial data for Matrix eQTL sample code: SNP location file.

Description

Arguments

Format

References

See Also