IsomirDataSeq: Class that contains all isomiRs annotation for all samples

Description Details Examples

View source: R/AllClasses.R


The IsomirDataSeq is a subclass of SummarizedExperiment::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.


IsomirDataSeqFromFiles creates this object using seqbuster output files.

Methods for this objects are isomiRs::counts() to get count matrix and isomiRs::isoSelect() for miRNA/isomiR selection. Functions available for this object are isomiRs::isoCounts() for count matrix creation, isomiRs::isoNorm() for normalization, isomiRs::isoDE() for differential expression and isomiRs::isoPLSDA() for clustering. isomiRs::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 metadata(ids)[['isoList']][[1]]$t5sum.

The naming of isomiRs follows these rules:

In general nucleotides in UPPER case mean insertions respect to the reference sequence, and nucleotides in LOWER case mean deletions respect to the reference sequence.

[['isoList']: R:['isoList' [1]: R:1


path <- system.file("extra", package="isomiRs")
fn_list <- list.files(path, full.names = TRUE)
de <- data.frame(row.names=c("f1" , "f2"),
                 condition = c("newborn", "newborn"))
ids <- IsomirDataSeqFromFiles(fn_list, coldata=de)


isomiRs documentation built on May 2, 2018, 4:05 a.m.