[Topic-models] Fwd: Topic model R package error

Duygu Dede ddede at baskent.edu.tr
Tue Mar 7 03:46:02 EST 2017


I am working on a bioinformatic project in which we would like to implement
topic model on k-mer representation of sequence data.
It means that a k-mer correspond to a term, a sequence sample correspond to
a document in text mining.
Attached file ("input_data") is an example of sample k-mer matrix for
4-mers that consists of 199 samples and 136 k-mers (each element of matrix
is k-mer occureneces of this k-mer in related sample).
When I run "LDA" function of "topicmodel" package in R 3.3.2 (x64) with
parameters below:

ldaOut <-LDA(input_data,k=20, method="Gibbs", control = list(alpha = 50/k,
estimate.beta = TRUE,
verbose = 1, prefix = tempfile(), save = 0, keep = 0,
seed = as.integer(Sys.time()), nstart = 1, best = TRUE,
delta = 0.1,
iter = 1000, burnin = 0, thin = 1000)

The error ("error.png")given as attached file is shown on the screen.

Thanks in advance for any suggestion or help

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