estimateSF: estimate size factor

In ph-pham/RepSeq: Analysis of High-throughput sequencing repertoire data (RepSeqTools)

Description

function

Usage

estimateSF(
  x,
  level = c("VpJ", "CDR3aa"),
  method = c("Chao", "iChao", "worChao", "Chao.gmmean", "Chao.median"),
  UsePseudoRef = TRUE
)

Arguments

x	an object of class RepSeqExperiment
level	level of repertoire to analyze VpJ, VJ, V, J, CDR3aa.
method	normaliztion method used for size factor computation.
UsePseudoRef	a boolean indicating if Chao indices will be computed according to a reference repertoire (geometric mean repertoire across all samples).

Value

a vector of normalized size factors

ph-pham/RepSeq documentation built on Dec. 22, 2021, 7:47 a.m.