Description Usage Arguments Value Examples

Helper function to adjust proportions for pre-existing allelic bias and also to obtain estimate of proportion variance based on attenuated read counts (adding pseudocount of 0.5 to each allele in each sample).

1 2 | ```
shiftAndAttenuateProportions(countsMat, totalsMat, probsMat, rhosMat,
checkArgs = FALSE)
``` |

`countsMat` |
matrix of observed major allele counts. Each row represents a specific genomic locus, while each column represents a set of observed major allele counts across loci (in practice, multiple columns represent different outcomes of count simulations). |

`totalsMat` |
matrix of total read counts across both alleles. The interpretation of rows and columns is the same as for countsMat. |

`probsMat` |
matrix of underlying probabilites of observing the major allele. The interpretation of rows and columns is the same as for countsMat. |

`rhosMat` |
matrix of dispersion parameters of beta distributions for each locus. The interpretation of rows and columns is the same as for countsMat. |

`checkArgs` |
single boolean specifying whether arguments should be checked for adherence to specifications. DEFAULT: FALSE |

a list with 2 elements:

`propsShifted` |
a 1-row marix of shifted major allele frequencies |

`propsShiftedVars` |
a 1-row matrix of estimated variances of obtained MAF estimates |

1 2 3 | ```
SNVCoverageTumor=sample(10:100,10) ## 2 genes with 5 loci each
SNVAllele1CountsTumor=rbinom(length(SNVCoverageTumor), SNVCoverageTumor, 0.5)
MBASED:::shiftAndAttenuateProportions(countsMat=matrix(SNVAllele1CountsTumor, ncol=2), totalsMat=matrix(SNVCoverageTumor, ncol=2), probsMat=matrix(rep(0.5, length(SNVCoverageTumor)), ncol=2), rhosMat=matrix(rep(0, length(SNVCoverageTumor)), ncol=2))
``` |

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