Define a proliferation score
proliferation_analysis.RdDefine a proliferation score on the basis of G1/S and G2/M markers (by default gsls_Symbol$Tirosh)
Usage
proliferation_analysis(
scMuffinList = NULL,
mc.cores = 1,
nbins = 25,
nmark_min = 5,
ncells_min = 5,
k = 99,
kmin = 49,
score_type = c("relative", "mean"),
mean_scale = TRUE,
gsl = NULL
)Arguments
- scMuffinList
scMuffinList object
- mc.cores
number of cores
- nbins
number of bins to split the distribution of average gene expression
- nmark_min
number of minimum markers that are required for the succesful calculation of a signature
- ncells_min
number of minimum cells in which a gene set has to be succesfully calculated
- k
number of permutations
- kmin
minimum number of permutations; due to missing values it is hard to ensure that a signature can be compared to k permutations in every cell
- score_type
type of score. if "relative", then the score is the difference between the observed gene set average expression and that of a k permutations; if "mean" the score is equal to the observed gene set average expression
- mean_scale
whether to scale the values obtained using score_type="mean"
- gsl
list with two gene sets with 1/S and G2/M markers. If NULL gsls_Symbol$Tirosh is used. See gsls_Symbol$Tirosh to properly format custom gene sets.