View source: R/VariantSelection_Quantile.R
VariantSelection_Quantile | R Documentation |
We get variants of interest using the quantile thresholding. This function is adapted from the Peter van Galen. Source: https://github.com/petervangalen/MAESTER-2021
VariantSelection_Quantile(
SE,
min_coverage = 2,
quantiles = c(0.1, 0.9),
thresholds = c(0.1, 0.9),
min_quality = NULL,
mean_allele_frequency = 0,
remove_nocall = FALSE,
verbose = TRUE
)
SE |
SummarizedExperiment object. |
min_coverage |
Minimum coverage needed. |
quantiles |
The lower and upper quantile you want to use. |
thresholds |
The VAF thresholds you want to use for the quantiles. |
min_quality |
The minimum quality you want for the Variants of Interest. Can be ignored by setting it to NULL. |
mean_allele_frequency |
The minimum mean allele frequency. Default = 0 |
remove_nocall |
Should NoCall cells (consensus = 0) be disregarded during the analysis? |
verbose |
Should the function be verbose? Default = TRUE |
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