CSeQTL_run_MatrixEQTL

Perform bulk and cell type-specific expression quantitative trail loci mapping with our novel method (Little et al. (2023) <doi:10.1038/s41467-023-38795-w>).

Paul Little

CSeQTL

Cell Type-Specific Expression Quantitative Trail Loci Mapping

CSeQTL_run_MatrixEQTL function

<dl><dt>TREC</dt>
<dd>A matrix of integer total read counts, rows are genes
with row labels with syntax "gene_name:chrom:start:end", 
columns are samples with column labels.</dd>
<dt>RD</dt>
<dd>A positive numeric vector of library sizes per sample.</dd>
<dt>XX</dt>
<dd>A numeric design matrix of baseline covariates 
including the intercept in the first column and centered 
continuous covariates.</dd>
<dt>SNP</dt>
<dd>An integer matrix, rows are genomic loci with row labels
such as "chrom:pos", columns correspond to samples with column labels.</dd>
<dt>out_cis_fn</dt>
<dd>A full path filename string to store
MatrixEQTL output</dd>
<dt>cisDist</dt>
<dd>A positive integer for number of SNPs to
include relative to the gene body</dd></dl>

Arguments

CSeQTL_run_MatrixEQTL — CSeQTL_run_MatrixEQTL

<dl>

<dt>TREC</dt>
<dd>A matrix of integer total read counts, rows are genes
with row labels with syntax "gene_name:chrom:start:end", 
columns are samples with column labels.</dd>


<dt>RD</dt>
<dd>A positive numeric vector of library sizes per sample.</dd>


<dt>XX</dt>
<dd>A numeric design matrix of baseline covariates 
including the intercept in the first column and centered 
continuous covariates.</dd>


<dt>SNP</dt>
<dd>An integer matrix, rows are genomic loci with row labels
such as "chrom:pos", columns correspond to samples with column labels.</dd>


<dt>out_cis_fn</dt>
<dd>A full path filename string to store
MatrixEQTL output</dd>


<dt>cisDist</dt>
<dd>A positive integer for number of SNPs to
include relative to the gene body</dd>

</dl>

CSeQTL_run_MatrixEQTL: CSeQTL_run_MatrixEQTL

Description

Usage

Value

Arguments