RAIDS-package: RAIDS: Ancestry Inference from Cancer Sequencing

In belleau/aicsPaper: Accurate Inference of Genetic Ancestry from Cancer Sequencing

RAIDS: Ancestry Inference from Cancer Sequencing

Description

The RAIDS package implements specialized algorithms that enable ancestry inference from various cancer sequencing sources (RNA, Exome and Whole-Genome sequencing).

Details

The RAIDS package also implements simulation algorithm that generates synthetic cancer-derived data.

This code and analysis pipeline was designed and developed for the following publication:

Author(s)

Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

Maintainer: Pascal Belleau <[e-mail]>

References

Belleau, P, Deschênes A, Tuveson DA, Krasnitz A. Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms. bioRxiv 2022.02.01.478737 [link to bioRxiv](https://doi.org/10.1101/2022.02.01.478737)

See Also

• prepPed1KG This function extracts the needed information from the 1000 Genomes pedigree file and formats it into a data.frame so in can be used in following steps of the ancestry inference process.

• generateMapSnvSel The function applies a cut-off filter to the SNP information file to retain only the SNP that have a frequency superior or equal to the specified cut-off in at least one super population.

• generateGDS1KG This function generates the GDS file that will contain the information from 1KG.

• identifyRelative The function identify patients that are genetically related in the GDS 1KG file.

• addRef2GDS1KG This function adds the information about the unrelated patients to the GDS 1KG file.

• add1KG2SampleGDS TODO

• addBlockFromPlink2GDS TODO

• addPhase1KG2SampleGDSFromGDS TODO

• appendStudy2GDS1KG TODO

• basePCASample TODO

• computeAlleleFraction TODO

• computeAllelicFractionDNA TODO

belleau/aicsPaper documentation built on Aug. 4, 2022, 1:12 a.m.