This function loads the allele count table and save it to a H5 file.
parse_table(file, h5_file = "mut.h5", ...)a string of the allele count table file directory.
a string of the output h5 file directory.
other parameters passed to fread.
a string of the output h5 file directory.
The allele count table should be a data.table with the following columns:
a string of the locus
a string of the cell barcode.
a integer of the forward depth.
a integer of the reverse depth.
a string of the alternative base.
a string of the reference base.
a integer of the coverage.
## Use the example data
f <- system.file("extdata", "mini_dataset.tsv.gz", package = "scMitoMut")
## Create a temporary h5 file
## In real case, we keep the h5 in project folder for future use
f_h5_tmp <- tempfile(fileext = ".h5")
## Load the data with parse_table function
f_h5 <- parse_table(f, sep = "\t", h5_file = f_h5_tmp)
f_h5
#> [1] "/tmp/RtmppwH5Ub/file2395d1147fb05.h5"
## open the h5 file and create a mtmutObj object
x <- open_h5_file(f_h5)
x
#> mtmutObj object
#> -------------------------------------------------
#> h5 file: /tmp/RtmppwH5Ub/file2395d1147fb05.h5
#> Available loci: 16
#> Selected loci: 16
#> Available cells: 1359
#> Selected cells: 1359
#> Loci passed the filter: 0
#> filter parameters:
#> min_cell: 1
#> model: bb
#> p_threshold: 0.05
#> alt_count_threshold: 0
#> p_adj_method: fdr