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 a linear model.
In the first step of GWAS, single nucleotide polymorphisms (SNPs) are
clumped according to their correlations and distances.
Then, SLOPE is performed on the data where each clump has
one representative.
Malgorzata Bogdan, Ewout van den Berg, Chiara Sabatti, Weijie Su
and Emmanuel Candes (2014)
"SLOPE - Adaptive Variable Selection via Convex Optimization"
<arXiv:1407.3824>.

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 <code>screeningResult</code>.</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 <code>screeningResult</code>.</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