is_ideal_bin will apply a set of bin-wise filters, based on high count outliers, high or low gc outliers, minimum read counts, minimum mappability, or maximum allowable frequency of N bases per bin.
Usage
is_ideal_bin(
counts,
gc,
n_freq,
map = NULL,
min_reads = 0,
max_N_freq = 0.05,
reads_outlier = 0.01,
gc_outlier = 0.001,
min_map = 0.9
)Arguments
- counts
Vector of bin counts for single cell
- gc
Vector of gc content
- n_freq
Vector of bin N frequency (proportion of N bases in a bin)
- map
Vector of bin mappability
- min_reads
Minimum number of reads to consider a bin
- max_N_freq
Maximum allowable frequency of N bases to consider a bin. Range (0, 1)
- reads_outlier
Flag bins with reads in the top quantile given by this value. Range (0, 1)
- gc_outlier
Flag bins with GC content in the top and bottom quantule given by this value. Range (0, 1)
- min_map
Minimum allowable mappability score for a bin. Range (0, 1)