Class that contains all isomiRs annotation for all samples
IsomirDataSeq is a subclass of
used to store the raw data, intermediate calculations and results of an
miRNA/isomiR analysis. This class stores all raw isomiRs
data for each sample, processed information,
summary for each isomiR type,
raw counts, normalized counts, and table with
experimental information for each sample.
IsomirDataSeqFromFiles creates this object using seqbuster output files.
Methods for this objects are
counts to get count matrix
for miRNA/isomiR selection. Functions
available for this object are
isoCounts for count matrix creation,
isoNorm for normalization,
differential expression and
isoPLSDA for clustering.
isoPlot helps with basic expression plot.
metadata contains two lists:
rawList is a list with same
length than number of samples and stores the input files
for each sample;
isoList is a list with same length than
number of samples and stores information for each isomiR type summarizing
the different changes for the different isomiRs (trimming at 3',
trimming a 5', addition and substitution). For instance, you can get
the data stored in
isoList for sample 1 and 5' changes
with this code
1 2 3 4 5 6