simulation_Ic {BioTIP} | R Documentation |
simulate x
loci B
to calculate the Ic score, where x should be the same as the length of identified BioTiP and B is self-defined.
simulation_Ic(obs.x, sampleL, counts, B = 1000)
obs.x |
A integer, length of identified BioTiP |
sampleL |
A list of vectors, whose length is the number of states. Each vector gives the sample names in a state. Note that the vector s (sample names) has to be among the column names of the R object 'df'. |
counts |
A numeric matrix or dataframe in which columns are samples and rows are transcripts. Each row needs to have a unique row name (i.e. transcript ID) |
B |
A integer, setting the permutation with |
A matrix of y
rows and B
columns where y
is the length of sampleL and B
is self-defined. Each column is a set of Ic scores calculated for each state
Zhezhen Wang zhezhen@uchicago.edu
counts = matrix(sample(1:100,27),3,9) colnames(counts) = 1:9 row.names(counts) = c('loci1','loci2','loci3') cli = cbind(1:9,rep(c('state1','state2','state3'),each = 3)) colnames(cli) = c('samples','group') samplesL <- split(cli[,1],f = cli[,'group']) simulation_Ic(2,samplesL,counts,B =3)