segment: segment(sourceData, namesArray, filterThreshold) creates...

In julianstanley/intsegments: Interactive Segments

Description

segment(sourceData, namesArray, filterThreshold) creates segments with CNSeg from raw data

Usage

segment(sourceData, namesArray, filterThreshold)

Arguments

sourceData	(dataframe or matrix) the original segments table
namesArray	(array) contains 5 elements, in order: namesArray[1]: The column name identifying the segment's chromosome namesArray[2]: The column name identifying the genomic start location namesArray[3]: The column name identifying the genomic stop location namesArray[4]: The column name identifying the mean log2 ratio of the segment namesArray[5]: The column name identifying the sample that the segment represents
filterThreshold	(float) between 0 and 1.0, the threshold for filtering based on mean absolute deviation

Value

A filtered dataframe of consensus segments

Examples

# Read the raw segment data
data(segData)
segData <- subset(segData, segData$Type == "TotalCN")
segment(segData, 
c("Chromosome", "StartPosition", "StopPosition", 
"Median.Log2.Ratio", "FileName"), 0.8)

julianstanley/intsegments documentation built on June 7, 2019, 1:48 a.m.