View source: R/analyze_dataset.R
analyze_dataset | R Documentation |
Load all samples for a given dataset and produce a summary data frame showing
each sample's summary row-by-row, a list of processed input files, and a list
of processed samples. The entries in the processed-samples list and the rows
in the summary data frame will be sorted according to the ordering of loci in
locus_attrs
and by the sample attributes. Processed files are stored
separately (as there may be multiple samples per file) and named by input
file path. An error is thrown if any locus entries in the given dataset are
not found in the locus attributes data frame.
analyze_dataset(
dataset,
locus_attrs,
analysis_function = analyze_sample,
summary_function = summarize_sample,
ncores = cfg("ncores"),
known_alleles = NULL
)
dataset |
data frame of sample details as produced by prepare_dataset. |
locus_attrs |
data frame of locus attributes as produced by load_locus_attrs. |
analysis_function |
function to use when analyzing each sample's data frame into the filtered version Defaults to analyze_sample. |
summary_function |
function to use when summarizing each sample's full details into the standard attributes. Defaults to summarize_sample. |
ncores |
integer number of CPU cores to use in parallel for sample analysis. Defaults to one less than half the number of detected cores with a minimum of 1. If 1, the function will run without using the parallel package. |
known_alleles |
data frame of custom allele names as defined for load_allele_names. if NULL only the names automatically generated for the dataset summary will be used. |
list of results, with summary
set to the single summary data frame,
files
the processed sequence files, and samples
the per-sample data
frames.
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