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 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

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