IsomirDataSeq-class
(Package: isomiRs) :
Class that contains all isomiRs annotation for all samples
The IsomirDataSeq is a subclass of SummarizedExperiment 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.
● Data Source:
BioConductor
● Keywords:
● Alias: IsomirDataSeq, IsomirDataSeq-class
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This function parses output of seqbuster tool to allow isomiRs/miRNAs analysis of samples in different groups such as characterization, differential expression and clustering. It creates an IsomirDataSeq object.
● Data Source:
BioConductor
● Keywords:
● Alias: IsomirDataSeqFromFiles
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counts
(Package: isomiRs) :
Accessors for the count matrix of a IsomirDataSeq object.
The counts slot holds the count data as a matrix of non-negative integer count values, one row for each isomiR, and one column for each sample. The normalized matrix can be obtained by using the parameter norm=TRUE.
● Data Source:
BioConductor
● Keywords:
● Alias: counts, counts,IsomirDataSeq-method, counts.IsomirDataSeq, counts<-,IsomirDataSeq,matrix-method
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isoCounts
(Package: isomiRs) :
Create count matrix with different summarizing options
This function collapses isomiRs into different groups. It is a similar concept than how to work with gene isoforms. With this function, different changes can be put together into a single miRNA variant. For instance all sequences with variants at 3' end can be considered as different elements in the table or analysis having the following naming hsa-miR-124a-5p.iso.t3:AAA.
● Data Source:
BioConductor
● Keywords:
● Alias: isoCounts
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isoDE
(Package: isomiRs) :
Differential expression analysis with DESeq2
This function does differential expression analysis with DESeq2-package using the specific formula. It will return a DESeqDataSet object.
● Data Source:
BioConductor
● Keywords:
● Alias: isoDE
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isoNorm
(Package: isomiRs) :
Normalize count matrix
This function normalizes raw count matrix using rlog function from DESeq2-package.
● Data Source:
BioConductor
● Keywords:
● Alias: isoNorm
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isoPLSDA
(Package: isomiRs) :
Partial Least Squares Discriminant Analysis for code{link{IsomirDataSeq
Use PLS-DA method with the normalized count data to detect the most important features (miRNAs/isomiRs) that explain better the group of samples given by the experimental design. It is a supervised clustering method with permutations to calculate the significance of the analysis.
● Data Source:
BioConductor
● Keywords:
● Alias: isoPLSDA
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isoPLSDAplot
(Package: isomiRs) :
Plot components from isoPLSDA analysis (pairs plot)
Plot the most significant components that come from isoPLSDA analysis together with the density of the samples scores along those components.
● Data Source:
BioConductor
● Keywords:
● Alias: isoPLSDAplot
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isoPlot
(Package: isomiRs) :
Plot the amount of isomiRs in different samples
This function plot different isomiRs proportion for each sample. It can show trimming events at both side, additions and nucleotides changes.
● Data Source:
BioConductor
● Keywords:
● Alias: isoPlot
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isoPlotPosition
(Package: isomiRs) :
Plot nucleotides changes at a given position
This function plot different isomiRs proportion for each sample at a given position focused on the nucleotide change that happens there.
● Data Source:
BioConductor
● Keywords:
● Alias: isoPlotPosition
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