compute_deletions: Compute the distribution of deletion sizes by segment
In milaboratory/mirutil:

Computes the histogram of segment trimming sizes for various segments: 'V3', 'D5', 'D3' or 'J5'. In case metadata is provided, segments applicable to computing mean deletion/trimming size are deduced from the list of chains present in data. Note that values for trimmings are negative, however, positive values are recorded in case of P-segments - polyndromic duplications.

1	compute_deletions(sample, metadata = NA)

`sample`	clonotype table, imported using 'read_mixcr_dataset' or 'read_mixcr_sample' functions
`metadata`	metadata, a named list with chain identifiers stored under the 'chain' entry - a comma-separated list of chains such as 'TRA', 'TRB', etc is expected. If set to NA will assume all chains are present

deletion size by segment 2D histogram/table with unweighted 'freq.clonotypes' and weighted 'freq.reads' frequencies, unnormalized 'count.*' values are also provided

milaboratory/mirutil documentation built on May 20, 2019, 1:24 p.m.