read_exposure

Read an exposure matrix from a file.

Utility functions for mutational signature analysis
as described in Alexandrov, L. B. (2020)
<doi:10.1038/s41586-020-1943-3>.
This package provides two groups of functions. One is
for dealing with mutational signature "exposures"
(i.e. the counts of mutations in a sample that are
due to each mutational signature). The other group of
functions is for matching or comparing sets of
mutational signatures. 'mSigTools' stands for
mutational Signature analysis Tools.

Steven Rozen

mSigTools

Mutational Signature Analysis Tools

Nanhai Jiang

read_exposure function

<dl><dt>file</dt>
<dd>File path to a CSV file containing an exposure matrix, i.e.
the numbers of mutations due to each mutational signature.
Each row corresponds to a mutational signature an each
column corresponds to a tumor or other biological sample.</dd>
<dt>check.names</dt>
<dd>Passed to <code>read.csv</code>.
IMPORTANT: If <code>TRUE</code> this will replace the double
colon in identifiers of the form &lt;tumor_type&gt;::&lt;sample_id&gt;
with two periods (i.e. &lt;tumor_type&gt;..&lt;sample_id&gt;.
If <code>check.names</code> is true, generate a warning
if double colons were present.</dd></dl>

Arguments

Read an exposure matrix from a file. — read_exposure

<dl>

<dt>file</dt>
<dd>File path to a CSV file containing an exposure matrix, i.e.
the numbers of mutations due to each mutational signature.
Each row corresponds to a mutational signature an each
column corresponds to a tumor or other biological sample.</dd>


<dt>check.names</dt>
<dd>Passed to <code>read.csv</code>.
IMPORTANT: If <code>TRUE</code> this will replace the double
colon in identifiers of the form &lt;tumor_type&gt;::&lt;sample_id&gt;
with two periods (i.e. &lt;tumor_type&gt;..&lt;sample_id&gt;.
If <code>check.names</code> is true, generate a warning
if double colons were present.</dd>

</dl>

read_exposure: Read an exposure matrix from a file.

Description

Usage

Value

Arguments

Examples