iseqr_exp_cl: iseqr_exp_cl
In ahopki14/tcrSeqR: Tools for analyzing data from Adaptive's ImmunoSeq platform

Description Usage Arguments Value Note Author(s)

Calculates the number of clones that expand relative to a baseline sample in a tcr experiment

1 2	iseqr_exp_cl(ds, comps, category = "type", alpha = 0.05, min.count = 5, output = "tcr")

`ds`	A tcr object
`comps`	A list of comparison types
`category`	The field to look for 'comps'. Default: type
`alpha`	The threshold over which clones with BH adjusted p-values will be considered 'expanded'. Default: 0.05
`min.count`	The minimum number of clones (sum of both samples) to be included in the analysis, Default: 5

If output=tcr, a tcr object with the number of expanded clones merge into the dataset. If output='nums', a data.frame with the number of expanded clones for each comparison. If output='p_vals', a matrix (ncol(assay(ds)) x length(patients)) with the p-values for each clone in each comparison.

It is not recommended (but not STRICTLY enforced) that you use the same baseline sample for comparisons (i.e. the first elements of all items in comps should be the same). If you REALLY know what you are doing, then you could use multiple baseline samples.

If output='p_vals', then only one comparison can be made at a time (length(comps) should be 1).

Alexander Hopkins

ahopki14/tcrSeqR documentation built on May 16, 2019, 6:56 p.m.