SomatiCAFormat

SomatiCAFormat-methods

SomatiCAFormat,character-method

SomatiCAFormat,data.frame-method

SomatiCAFormat,GRanges-method


Convert a data frame or read a file into SomatiCA input format. Remove missing values from input, check validity of data type and convert it into SomatiCA input format, which is a GRanges object. 


methods

 ~~ other possible keyword(s) ~~ 

SomatiCA is a software suite that is capable of
identifying, characterizing, and quantifying somatic CNAs from
cancer genome sequencing. First, it uses read depths and lesser
allele frequencies (LAF) from mapped short sequence reads to
segment the genome and identify candidate CNAs. Second,
SomatiCA estimates the admixture rate from the relative
copy-number profile of tumor-normal pair by a Bayesian finite
mixture model. Third, SomatiCA quantifies absolute somatic
copy-number and subclonality for each genomic segment to guide
its characterization. Results from SomatiCA can be further
integrated with single nucleotide variations (SNVs) to get a
better understanding of the tumor evolution.

Mengjie Chen

SomatiCA

SomatiCA: identifying, characterizing, and quantifying somatic
copy number aberrations from cancer genome sequencing

SomatiCAFormat-methods function

<dl> <dt><code>signature(data = "character")</code></dt><dd>
Filename.
</dd> <dt><code>signature(data = "data.frame")</code></dt><dd>
Data frame with 7 column (tumor sample with control), including seqnames, start, zygosity, tCount, LAF, tCountN, germLAF. 
</dd> <dt><code>signature(data = "GRanges")</code></dt><dd>
A GRange object. 
</dd> </dl>

Methods

 ~~ Methods for Function <code>SomatiCAFormat</code> in Package <span class = "pkg">SomatiCA</span> ~~

 ~~ Methods for Function <code>SomatiCAFormat</code> in Package <span class="pkg">SomatiCA</span> ~~

SomatiCAFormat-methods: Methods for Function `SomatiCAFormat` in Package SomatiCA

Description

Arguments

Methods