SATS (version 1.0.6)

GenerateLMatrix: Generate an L Matrix

Description

Generation of the L matrix.

Usage

GenerateLMatrix(Panel_context, Patient_Info)

Value

A data frame (L matrix) of 96 by N, where N is the number of tumors.

Arguments

Panel_context

A data frame returned from GeneratePanelSize.

Patient_Info

A data frame with columns 'PATIENT_ID' and 'SEQ_ASSAY_ID'.

Author

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

Details

The GenerateLMatrix() function relies on the 'Patient_Info' data frame to link each patient to their specific sequencing assay, identified by 'SEQ_ASSAY_ID'. This is the same core information required by the genomic_information argument in the GeneratePanelSize() function. The values in the 'SEQ_ASSAY_ID' column will be used as the column names for the resulting L matrix, ensuring each column corresponds to a unique sample.

It is important to understand the distinction between the two functions. GeneratePanelSize() is a simpler utility that only calculates the total size (in base pairs) of each panel type and does not require patient-level information. However, to generate the correctly dimensioned L matrix with the proper trinucleotide contexts for each specific sample, you must call GenerateLMatrix().

See Also

GeneratePanelSize

Examples

data(SimData, package="SATS")

Panel_context <- GeneratePanelSize(genomic_information=SimData$PanelEx, Class="SBS", 
                         SBS_order="COSMIC")
L_mat <- GenerateLMatrix(Panel_context, SimData$PatientInfo) 
# For more detailed usage, please refer to README and the user manual
# in https://github.com/binzhulab/SATS/tree/main.