Prepare depth tables from a single resolution-specific input

Reads and validates a precalculated depth data frame or delimited file, detects its subtype resolution from the denominator context column, and derives all lower-resolution depth tables that can be recovered from that input.

Usage

write_depth_data(depth_data, d_sep = "\t", group_cols = "sample")

Arguments

depth_data

A data frame or path to a delimited file. It must contain the columns named in group_cols, subtype_depth, and exactly one context column from denominator_dict for base_6, base_12, base_96, or base_192.

d_sep

A single-character delimiter used to read depth_data when it is a file path.

group_cols

Character vector of columns that identify independent groups in depth_data. Defaults to "sample"; use other columns when depth data is already aggregated to those groups.

Value

A named list of the depth tables at available subtype resolutions: "base192", "base96", "base12", "base6", "global" (none). Each subtype table contains the group_cols, its denominator_dict context column, subtype_depth, and group_depth; the global table contains group_cols and group_depth.

Details

The input must contain the grouping columns, subtype_depth, and the appropriate context column. Use MutSeqR::denominator_dict to see the context column name associated with each subtype resolution. Each group must have exactly one row for every context in MutSeqR::context_list at the given resolution; contexts with zero depth must be included explicitly. Duplicate group-context pairs, unknown contexts, missing contexts, or non-finite per-group depth totals produce an error.

Base192 input produces Base96, Base12, Base6, and global depth tables. Base96 input produces Base6 and global tables, but cannot produce Base12 because its normalized contexts have already combined reverse-complement strands. Base12 input produces Base6 and global tables. Base6 input produces global depth.