Import Tapestri H5 data and extract genotype matrix
tapestri_h5_to_sce.RdImport Tapestri H5 data and extract genotype matrix
Usage
tapestri_h5_to_sce(
file,
GT_cutoff = 35,
VAF_cutoff = 5,
DP_cutoff = 10,
GQ_cutoff = 30,
AF_cutoff = 25,
variant_set = NULL,
protein = TRUE
)Arguments
- file
path to the h5 file
- GT_cutoff
Fraction of cells that are successfully genotyped for initial filtering (default 0.2, meaning 20%)
- VAF_cutoff
Fraction of cells that are mutated for initial filtering of variants (default 0.005, meaning 0.05%)
- DP_cutoff
minimum number of reads necessary for a reliable genotype call in a single cell (default: 10)
- GQ_cutoff
minimum genotype quality necessary for a reliable genotype call in a single cell (default: 30)
- AF_cutoff
Deviation from 0, 50, or 100% for a reliable call of WT, Het or Hom respectively (default: 25)
- variant_set
character vector of variants to be included in the format output by mission bio.
- protein
logical, whether protein data should be included. default=TRUE
- return_variants_only
logical,