GereratePanelSize: Generate Panel Size Matrix

In SATS: Signature Analyzer for Targeted Sequencing (SATS)

Generate Panel Size Matrix

Description

Generation of the panel size matrix given the panel information.

Usage

 GeneratePanelSize(genomic_information, Types)

Arguments

genomic_information	Data frame of panel information (see details).
Types	Mutation type order either one of "COSMIC" or "signeR" (see details).

Details

The first argument 'genomic_information' should contain columns 'Chromosome', 'Start_Position', 'End_Position', 'SEQ_ASSAY_ID'. The column 'Chromosome' contains chromosome number where 'Start_Position' and 'End_Position' columns are start and end positions of the targeted panel. The last column 'SEQ_ASSAY_ID' distinguishes different panels consisting of the result. Please note that the column names of 'genomic_information' identical to 'Chromosome', 'Start_Position', 'End_Position', 'SEQ_ASSAY_ID'. The second argument specifies mutation type order as either one of "COSMIC" or "signeR" where "COSMIC" corresponds to the order from the COSMIC database v3.2 and "signeR" corresponds to the order from the signeR package. Note: The result of 'GeneratePanelSize()' may NOT be an 'L' matrix. The 'L' matrix can be constructed by attaching the columns of the function output that correspond to the columns of the 'V' matrix. The resulting augmented matrix can be used as the opportunity matrix for 'signeR()' function, 'L' matrix for 'EstimateSigActivity()' and 'CalculateSignatureBurdens()' functions. Therefore, it is important the mutation type order (row names) should be the same as input matrix (Mutation type matrix 'V'). We highly recommend to confirm that both 'V' and 'L' matrices have the same mutation type order corresponding to one of COSMIC database v3.2 or signeR package (both have the same order but have different expression) to conduct the consistent analysis.

Value

A data frame of 96 by 'S' (the number of panels, 'SEQ_ASSAY_ID') where entries denote the number of trinucleotides per million base pairs.

Author(s)

Donghyuk Lee <[e-mail]> and Bin Zhu <[e-mail]>

Examples

    data(SimData, package="SATS")

    GeneratePanelSize(genomic_information = SimData$PanelEx, Types = "COSMIC")
    GeneratePanelSize(genomic_information = SimData$PanelEx, Types = "signeR")

SATS documentation built on Aug. 8, 2025, 6:22 p.m.