Analysis of a DNA, RNA, or peptide sequence to understand its features, function, structure, or evolution.
2
votes
1answer
201 views
5
votes
2answers
140 views
Other substitution matrices for missing value state in sequence analysis with TraMineR?
We have a question about how to deal with missing values/gaps within sequences. We like to set up our own substitution-cost matrix for the Optimal Matching process. As far as we know, TraMiner allows ...
2
votes
0answers
30 views
What is the difference between emerging and discriminative patterns?
I'm working on a way to make efficient classification on sequential patterns mining algorithms. Looking in the state-of-the-art I found that there is two type of algorithm to address this problem : ...
2
votes
2answers
77 views
Modifying the time granularity of a state sequence
I created a sequence object from my SPELL-formatted data set. The sequence length of the sequence object is 1440 (i.e., 1-min intervals for a day).
Is there any easy way for TraMineR to convert the ...
2
votes
1answer
76 views
What is the relationship between substitution cost matrix and indel costs?
In TraMineR I might compute dissimilarities as such:
...
1
vote
0answers
47 views
Viterbi realignment
In the past I have trained Hidden Markov Models (HMMs) for sequence recognition with the Baum-Welch algorithm such that if there were $n$ classes, I would use training data $D_i$ for a class $i$ to ...
11
votes
4answers
767 views
Framing the negative binomial distribution for DNA sequencing
The negative binomial distribution has become a popular model for count data (specifically the expected number of sequencing reads within a given region of the genome from a given experiment) in ...
3
votes
1answer
104 views
Problems with Groups in Traminer
I'm having a problem using the group function in TraMineR. I have a data set that contains SPELL data, so multiple rows per case. I also have demographic data per case, at one row per case. I merge ...
2
votes
1answer
129 views
Optimal matching distances as percentages?
I'm using R and the library TraMineR to do sequence analysis on social science data. I have computed an optimal matching (OM) distance matrix.
...
2
votes
1answer
207 views
How to describe multi-channel sequence objects in TraMineR?
I have created a multi-channel object here:
https://github.com/aronlindberg/VOSS-Sequencing-Toolkit/blob/master/creating_multichannel_object.R
However, when I try to use various functions to ...
