summary_calls

Combine both autosomal and sex chromosomal analyses into one output

Usage

summary_calls(
  inChASM,
  minTotal = 60000,
  minPosterior = 0.95,
  ignoreUnusual = FALSE,
  printProtocol = FALSE
)

Arguments

inChASM

the result of combining both autosomal and sca analyses

minTotal

minimum total for autosomal or sca analyses

minPosterior

minimum value maxP can take (i.e. minimum posterior probability accepted)

ignoreUnusual

filter our unusual observations?

printProtocol

print protocol column?

Value

combined calls

Examples

example_calls <- runChASM(rawReadCountsIn = example_data)

summary_calls(inChASM = example_calls, minTotal = 6e4, minPosterior = 0.95)
#> # A tibble: 3 × 10
#>   sample  unusual flags autosomal_call sca_call C_call autosomal_total sca_total
#>   <chr>   <lgl>   <int> <chr>          <chr>    <chr>            <dbl>     <dbl>
#> 1 Ind_71… TRUE        4 No Aneuploidy  XXX      No Si…           70688     76444
#> 2 Ind_18… FALSE       1 No Aneuploidy  XXX      No Si…          209933    225713
#> 3 Ind_25… FALSE       0 Trisomy 21     XX       No Si…          254544    268132
#> # ℹ 2 more variables: automsomal_maxP <dbl>, sca_maxP <dbl>