get_col_num

This is an internal function to find the
column numbers of phenotypes when names
are put in instead of column numbers.

internal

Combined Analysis of Pleiotropy and Epistasis infers predictive
networks between genetic variants and phenotypes. It can be used with
standard two-parent populations as well as multi-parent populations, such
as the Diversity Outbred (DO) mice, Collaborative Cross (CC) mice, or the
multi-parent advanced generation intercross (MAGIC) population of Arabidopsis
thaliana. It uses complementary information of pleiotropic gene variants across
different phenotypes to resolve models of epistatic interactions between alleles.
To do this, cape reparametrizes main effect and interaction coefficients from
pairwise variant regressions into directed influence parameters. These
parameters describe how alleles influence each other, in terms of suppression
and enhancement, as well as how gene variants influence phenotypes. All of the
final interactions are reported as directed interactions between pairs of
parental alleles. For detailed descriptions of the methods used in this package
please see the following references.
Carter, G. W., Hays, M., Sherman, A. & Galitski, T. (2012) <doi:10.1371/journal.pgen.1003010>.
Tyler, A. L., Lu, W., Hendrick, J. J., Philip, V. M. & Carter, G. W. (2013) <doi:10.1371/journal.pcbi.1003270>.

Anna L Tyler

cape

Combined Analysis of Pleiotropy and Epistasis for Diversity
Outbred Mice

Anna Tyler

Jake Emerson

Baha El Kassaby

Ann Wells

Georgi Kolishovski

Vivek Philip

Gregory Carter

get_col_num function

<dl><dt>data_mat</dt>
<dd>a matrix with column names</dd>
<dt>col_which</dt>
<dd>a character string indicating which column should be identified
If col_which is numeric the number is returned.</dd>
<dt>dim_which</dt>
<dd>A number indicating whether the algorithm should look
in rows (1) or columns (2) for the name.</dd></dl>

Arguments

Find column numbers using column names — get_col_num

<dl>

<dt>data_mat</dt>
<dd>a matrix with column names</dd>


<dt>col_which</dt>
<dd>a character string indicating which column should be identified
If col_which is numeric the number is returned.</dd>


<dt>dim_which</dt>
<dd>A number indicating whether the algorithm should look
in rows (1) or columns (2) for the name.</dd>

</dl>

Find column numbers using column names

get_col_num: Find column numbers using column names

Description

Usage

Value

Arguments