Functions which act on chromR objects
masker(
x,
min_QUAL = 1,
min_DP = 1,
max_DP = 10000,
min_MQ = 20,
max_MQ = 100,
preserve = FALSE,
...
)variant.table(x)
win.table(x)
object of class chromR
minimum variant quality
minimum cumulative depth
maximum cumulative depth
minimum mapping quality
maximum mapping quality
a logical indicating whether or not to preserve the state of
the current mask field. Defaults to FALSE
arguments to be passed to methods
The function masker creates a logical vector that determines which variants are masked. By masking certain variants, instead of deleting them, it preserves the dimensions of the data structure until a change needs to be committed. Variants can be masked based on the value of the QUAL column of the vcf object. Experience seems to show that this value is either at its maximum (999) or a rather low value. The maximum and minimum sequence depth can also be used (mindp and maxdp). The default is to mask all variants with depths of less than the 0.25 quantile and greater than the 0.75 quantile (these are also known as the lower and upper quartile). The minimum and maximum mapping qualities (minmq, maxmq) can also be used.
This vector is stored in the var.info$mask slot of a chromR object.
The function variant.table creates a data.frame containing information about variants.
The funciton win.table