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MethFilterNorm

Function loading the methylation calls data into a MethylRaw or MethylRawList object (MethylKit package data types) and performing normalization and filtering of the data.

Version 1.0
Bundle sequencing
Categories Analysis
Authors Chiara Facciotto (chiara.facciotto@helsinki.fi)
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Requires R ; GenomicRanges (R-bioconductor) ; data.table (R-package) ; download (bash) ; methylKit
Source files component.xml MethFilterNorm.R
Usage Example with default values
Deprecated

This component is not part of the methylation pipeline anymore.

Inputs

Name Type Mandatory Description
methCallArray Array<CSV> Mandatory An array pointing to CSV files containing the methylation calls information. Each of these files must include the following columns:
- chr, the chromosome location in the format chr1
- pos, the position (1-based) of the cytosine inside the chromosome
- strand, the strand where the cytosine is located
- coverage, how many reads are aligned at that specific position
- freqC, the percentage of methylated cytosines aligned at that specific position.
groupIDs CSV Mandatory CSV file containg 2 columns:
- Key, the same sample IDs associated to the methCallArray array elements
- Treatment, a boolean value (0 or 1) denoting which samples belongs to one state (e.g. controls) which samples belongs to another (e.g. test).

Outputs

Name Type Description
rawFilteredNormMethyl BinaryFile RData file containing the methylRawList object to be used as input for DiffMeth component.
statistics Latex Directory containing plots related to coverage and methylation statistics before and after normalization and filtering.
analysis CSVList Directory containing CSV files with numCs, coverage and perc.meth information (one file per sample).
visualization BinaryFolder Directory containing the bedgraph files for the visualization. The positions are 0-based and every bedgraph file contains data for every sample but with different score value (either numCs, coverage or perc.meth).

Parameters

Name Type Default Description
assembly string "hg19" A string containing the assembly genome used during the alignment.
bedgraph boolean false Boolean value indicating if three bedgraph files should be printed in the visualization folder. Each of the three files contains a different parameter as score (respectivelly numCs, coverage and percMeth).
bothStrands boolean false Boolean value indicating whether the plots of coverage and methylation statistics should summarize either both strands in the same plot (FALSE) or produce two strand-specific plots (TRUE).
context string "" A string stating the methylation context. Allowed values are CpG, CHG, CHH or just the empty string "" in case the context is not relevant in the analysis.
dataFrame boolean false Boolean value indicating if CSV files summarizing the methylation information for every sample should be printed in the analysis folder.
hiThr float 0.999 An value for filtering the read counts. When the value is between 0 and 1 it indicates the percentage of reads that are aligned, while when it is higher than 1 it indicates the number of reads.
Bases having higher coverage than this value are discarded.
If the data don not have to be filtered, both loThr and hiThr must be set as NULL.
loThr float 10 An value for filtering the read counts. When the value is between 0 and 1 it indicates the percentage of reads that are aligned, while when it is higher than 1 it indicates the number of reads.
Bases having lower coverage than this value are discarded.
If the data don not have to be filtered, both loThr and hiThr must be set as NULL.
method string "median" String denoting the method used to calculate the scaling factor during normalization. Allowed values are median or mean.
normalize boolean true Boolean values stating if the coverage has to be normalized or not.

Test cases

Test case Parameters IN
methCallArray
IN
groupIDs
OUT
rawFilteredNormMethyl
OUT
statistics
OUT
analysis
OUT
visualization
case1_default (missing) methCallArray groupIDs rawFilteredNormMethyl (missing) (missing) (missing)
case2_method properties methCallArray groupIDs rawFilteredNormMethyl (missing) (missing) (missing)

# Testing MethFilterNorm component,
method=mean

case3_loThr_hiThr properties methCallArray groupIDs rawFilteredNormMethyl (missing) (missing) (missing)

# Testing MethFilterNorm component,
loThr=5,
hiThr=0.99,

case4_dataFrame_bedgraph properties methCallArray groupIDs rawFilteredNormMethyl (missing) analysis visualization

# Testing MethFilterNorm component,
loThr=10,
hiThr=0.999,
bedgraph=true,
dataFrame=true,


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