compute_segment_usage2: Compute 2D segment usage
In milaboratory/mirutil:

Computes the distribution of segment usage frequencies for a list of segment type pairs: 'VD', 'DJ' or 'VJ'. By default, all segments are analyzed. In case metadata is provided, applicable segment types are deduced from the list of chains present in data

1	compute_segment_usage2(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

segment pair usage 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.