EBSEA {EBSEA} | R Documentation |
EBSEA takes as input unnormalized counts of exons, normalizes them and then performs a two group comparison of the samples to detect differentially expressed between the groups. Both paired or unpaired comparison are supported. It calculates fold changes, p-values and false discovery rate of the genes between the groups.
EBSEA(data, group, paired = FALSE, plot = FALSE)
data |
A dataframe of exon count data |
group |
A vector indicating the sample groups in the experiment |
paired |
A logical indicating whether the samples are paired or unpaired. Default: FALSE |
plot |
A logical indicating whether a volcano plot is visualized. Default: FALSE |
EBSEA returns a list of two dataframes. ExonTable is a dataframe that contains exon statistics including log fold change, p-values, adjusted p-values, average expression and fold change. GeneTable is a dataframe that contains the corresponding fold change, log fold change, p-values and false discovery rate.
Laiho, A., & Elo, L. L. (2014). A note on an exon-based strategy to identify differentially expressed genes in RNA-seq experiments. PloS One, 9(12), e115964.
data(origCounts) group <- c('Group1', 'Group1', 'Group1', 'Group2', 'Group2', 'Group2', 'Group2') result <- EBSEA(origCounts, group)