Fit binomial mixture model for every candidate locus
run_model_fit(
mtmutObj,
mc.cores = getOption("mc.cores", 1L),
bb_over_bm = TRUE,
bb_over_bm_p = 0.05,
bb_over_bm_adj = "fdr"
)a mtmutObj object.
integer number of cores to use.
logical weather to use binomial mixture model result to define the wildtype cells for training beta binomial model.
numeric the binomial mixutre model p value threshold for selecting the wildtype cells for training beta binomial model.
string the method for adjusting the binomial mixture p value, default is "fdr".
NULL, the results are saved in the h5f file.
This function will fit three models for every candidate locus:
binomial mixture model
beta binomial model
binomial model
The results are saved in the h5f file.
## Use the example data
f <- system.file("extdata", "mini_dataset.tsv.gz", package = "scMitoMut")
## Load the data with parse_table function
f_h5_tmp <- tempfile(fileext = ".h5")
f_h5 <- parse_table(f, sep = "\t", h5_file = f_h5_tmp)
# open the h5f file
x <- open_h5_file(f_h5)
# run the model fit
run_model_fit(x)
#> chrM.200
#> chrM.204
#> chrM.310
#> chrM.824
#> chrM.1000
#> chrM.1001
#> chrM.1227
#> chrM.2285
#> chrM.6081
#> chrM.9429
#> chrM.9728
#> chrM.9804
#> chrM.9840
#> chrM.12889
#> chrM.16093
#> chrM.16147
#> used (Mb) gc trigger (Mb) max used (Mb)
#> Ncells 2127831 113.7 3221262 172.1 3221262 172.1
#> Vcells 4317620 33.0 10146329 77.5 10145363 77.5
x
#> mtmutObj object
#> -------------------------------------------------
#> h5 file: /tmp/RtmppwH5Ub/file2395d20549da.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
# Filter the loci based on the model fit results
x <- filter_loc(x, min_cell = 5, model = "bb", p_threshold = 0.05, p_adj_method = "fdr")
x
#> mtmutObj object
#> -------------------------------------------------
#> h5 file: /tmp/RtmppwH5Ub/file2395d20549da.h5
#> Available loci: 16
#> Selected loci: 16
#> Available cells: 1359
#> Selected cells: 1359
#> Loci passed the filter: 14
#> filter parameters:
#> min_cell: 5
#> model: bb
#> p_threshold: 0.05
#> alt_count_threshold: 0
#> p_adj_method: fdr