A matrix of count data of non-negative integer values.
The rows correspond to counts for each exon counting bin,
the columns correspond to samples. Note that biological
replicates should each get their own column, while the
counts of technical replicates (i.e., several sequencing
runs/lanes from the same sample) should be summed up
into a single column
alternativeCountData
DEXSeq can be also used for test for differences in exon inclusion
based on the number of reads supporting the inclusion of an exon and
the number of reads supporting the exclusion of an exon. A matrix of
count data of non-negative integer values.The rows correspond to exonic
regions and the columns correspond to samples. This matrix should contain
the number of exon-exon junction reads that skip each exon in each sample.
If NULL, then the sum of the other exons belonging to the same gene is
considered for testing (i.e. the normal DEXSeq approach).
countfiles
A character vector containing the path to the files that
were originated with the script 'dexseq_count.py'.
sampleData
A data.frame with the annotation (e.g. treatments, or tissue
types, or phenotypes, or the like). The number of rows in
the data frame must to be equal to the number of columns of
the countData matrix, assigning the annotation of each sample.
design
A formula which specifies the design of the experiment. It must
specify an interaction term between a variable from the sampleData
columns with the 'exon' variable. By default, the design
will be '~ sample + exon + condition:exon'. This formula indicates
the contrast between 'condition' and exon', i.e. differences in exon
usage due to changes in the 'condition' variable. See the vignette
for more examples of other designs.
featureID
A character vector of counting regions identifiers ordered according
to the rows in countData. The identifiers names can be repeated
between groups but not within groups.
groupID
A vector of group identifiers ordered according to its
respective row in countData. It must reflect the sets
of counting regions belonging to the same group, for
example, exon bins in belonging to the same gene should
have the same group identifier.
featureRanges
Optional. GRanges or GRangesList describing
the genomic coordinates of each of the rows of countData.
transcripts
Optional. A list of the same length as the number of
columns of countData. Each element of the list should contain
the transcript identifiers of the
flattenedfile
A character vector containing the path to the flattened annotation
file that was originated with the script 'dexseq_prepare_annotation.py'.
SE
A SummarizedExperiments object, originated using the function
SummarizeOverlaps. See examples for more details.