compute_deletions_m: Compute mean deletion sizes by segment
In milaboratory/mirutil:

Computes the means 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_m(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 table with unweighted 'mean.clonotypes' and weighted 'mean.reads' means, total number of clonotypes/reads for a given segment is stored in 'count.*' columns

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