This is an helper function that allows the user to
import counts, class (mandatory) and
variables (optional) data, and creates a
A tab-delimited file which contains RNA-Seq count data. Each row is a feature (i.e. gene, transcript, exon etc.) and each column is a sample
A tab-delimited file which contains experiment information. Each row is a sample and each column is a variable. This file must contain at least one column which represent 'class' information for data adjustment and classification; the class column must be labeled as 'class'
Before creating a
SummarizedExperiment object, the
function performs some checks on input data to ensure that only a
of raw counts is accordingly loaded. Other checks allows the
identification of missing data (NA) in the data frame of the variables
SummarizedExperiment object containing raw counts,
class and (optionally) variables of interest.
Mattia Chiesa, Luca Piacentini
Morgan M, Obenchain V, Hester J and Pag\'es H (2016). SummarizedExperiment: SummarizedExperiment container. R package version 1.4.0.
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rawdata.path <- system.file(package = "DaMiRseq","extdata") # import tab-delimited files: # sample data are a small subset of Genotype-Tissue Expression (GTEx) # RNA-Seq database (dbGap Study Accession: phs000424.v6.p1): count_data <- read.delim(file.path(rawdata.path, "counts_import.txt")) variables_data <- read.delim(file.path(rawdata.path, "annotation_import.txt")) # create a SummarizedExperiment object: SE <- DaMiR.makeSE(count_data, variables_data) print(SE)
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