read_phenotype

Reading phenotype data from file. It is assumed, that data is given in .fam file.
In this format, first column is family id (FID), second is individual id (IID),
third is Paternal individual ID (PAT), fourth is Maternal individual ID (MAT),
fifth is SEX and sixth and last is PHENOTYPE.
If file has only four columns, then it is assumed that PAT and MAT columns are missing.
If there is only one column, then it is assumed that only phenotype is provided.

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

read_phenotype function

<dl><dt>filename</dt>
<dd>character, name of file with phenotype</dd>
<dt>sep</dt>
<dd>character, field seperator in file</dd>
<dt>header</dt>
<dd>logical, does first row of file contain variables names</dd>
<dt>stringAsFactors</dt>
<dd>logical, should character vectors be converted to factors?</dd></dl>

Arguments

Read phenotype from .fam file — read_phenotype

<dl>

<dt>filename</dt>
<dd>character, name of file with phenotype</dd>


<dt>sep</dt>
<dd>character, field seperator in file</dd>


<dt>header</dt>
<dd>logical, does first row of file contain variables names</dd>


<dt>stringAsFactors</dt>
<dd>logical, should character vectors be converted to factors?</dd>

</dl>

read_phenotype: Read phenotype from .fam file

Description

Usage

Value

Arguments