clump_snps

Clumping procedure performed on SNPs, columns of matrix <code>X</code>, from
object of class <code>screeningResult</code>,
which is an output of function <code>screen_snps</code>.
SNPs are clustered based on their correlations. For details see package vignette.

Genome-wide association study (GWAS) performed with SLOPE,
short for Sorted L-One Penalized Estimation, a
method for estimating the vector of coefficients in linear model.
In the first step of GWAS, SNPs are clumped according to their correlations and
distances. Then, SLOPE is performed on data where each clump has
one representative.

Piotr Sobczyk

geneSLOPE

Genome-Wide Association Study with SLOPE

Damian Brzyski

Christine Peterson

Emmanuel J. Candes

Malgorzata Bogdan

Chiara Sabatti

clump_snps function

<dl><dt>screenResult</dt>
<dd>object of class screeningResult</dd>
<dt>rho</dt>
<dd>numeric, minimal correlation between two SNPs to be assigned to one clump</dd>
<dt>pValues</dt>
<dd>numeric vector, p-values for SNPs computed outside geneSLOPE,
eg. with EMMAX</dd>
<dt>verbose</dt>
<dd>logical, if TRUE (default) progress bar is shown</dd></dl>

Arguments

Clumping procedure for SLOPE — clump_snps

<dl>

<dt>screenResult</dt>
<dd>object of class screeningResult</dd>


<dt>rho</dt>
<dd>numeric, minimal correlation between two SNPs to be assigned to one clump</dd>


<dt>pValues</dt>
<dd>numeric vector, p-values for SNPs computed outside geneSLOPE,
eg. with EMMAX</dd>


<dt>verbose</dt>
<dd>logical, if TRUE (default) progress bar is shown</dd>

</dl>

clump_snps: Clumping procedure for SLOPE

Description

Usage

Value

Arguments