Write and read quality-control thresholds — write

write_thresholds() saves thresholds to a YAML file, and read_thresholds() reads them back. Use the file to apply the same quality-control policy to each study, or to load thresholds that you tuned in nacho_app(). The Export page of the app writes the same file.

Usage

write_thresholds(thresholds, file)

read_thresholds(file)

Arguments

thresholds: A list of thresholds, as returned by nacho_thresholds() or found in the @thresholds property of a nacho object.
file: The path of the YAML file.

Value

write_thresholds() returns file, invisibly. read_thresholds() returns the list of thresholds.

Details

In the file, .inf and -.inf are open bounds, and .na.character is an unknown instrument. You can edit the file by hand. read_thresholds() reads whole numbers such as 80 as numbers, and checks the thresholds as normalise() does. If the file does not give a miRNA threshold (Ligation_order, Ligation_R2, Ligation_NEG or Haemolysis), read_thresholds() uses the value of the preset in the file.

Examples

file <- tempfile(fileext = ".yml")
thresholds <- nacho_thresholds("sprint")
thresholds$FoV <- 80
write_thresholds(thresholds, file)
read_thresholds(file)
#> $preset
#> [1] "nsolver"
#> 
#> $instrument
#> [1] "sprint"
#> 
#> $BD
#> [1] 0.1 1.8
#> 
#> $FoV
#> [1] 80
#> 
#> $PCL
#> [1] 0.95
#> 
#> $LoD
#> [1] 2
#> 
#> $Positive_factor
#> [1] 0.3 3.0
#> 
#> $House_factor
#> [1]  0.1 10.0
#> 
#> $Housekeeping_detected
#> [1] 3
#> 
#> $Ligation_order
#> [1] 1
#> 
#> $Ligation_R2
#> [1] 0.95
#> 
#> $Ligation_NEG
#> [1] -Inf    0
#> 
#> $Haemolysis
#> [1] -Inf  Inf
#> 
unlink(file)