Up: Component summary Function

DiffExprSeq

For differential expression at gene and exon level of RNA-Seq data. You can use HTSeqBam2Counts to prepare the suitable inputs for this function.

Version 1.0
Bundle sequencing
Categories
Authors Alejandra Cervera (alejandra.cervera@helsinki.fi)
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Source files component.xml function.scala
Usage Example with default values
Deprecated

The exon part is outdated, and the standard case is the same as DEan.

Inputs

Name Type Mandatory Description
exonCounts Array<BinaryFile> Optional The alignment counts for each exon
geneCounts Array<BinaryFile> Optional The alignment counts for each gene
annotation GFF Optional Provides the gene annotations in GFF format. These files can be obtained from a GTF annotation file using HTSeqBam2Counts function.
conditions CSV Optional A csv with at least one column named Condition with the conditions to be tested. The list should be in the same order as the count files in the input arrays. If defined then conditionList parameter is ignored.

Outputs

Name Type Description
exon CSV Table with the results of the exon level analysis
gene CSV Table with the results of the gene level analysis

Parameters

Name Type Default Description
conditionList string "A,A,B,B" A comma separated list of conditions to be tested for differential expression in the same order as the samples. Example: conditionA,conditionA,conditionB,conditionB
level string "Exon" Level at which the differential expression is obtained. Possible values "Exon,Gene", "Exon" or "Gene".
minCount int 5 Minimum number of reads covering the exon to be considered.
nCores int 5 Number of threads for the analysis

Test cases

Test case Parameters IN
exonCounts
IN
geneCounts
IN
annotation
IN
conditions
OUT
exon
OUT
gene
case1_exon properties exonCounts (missing) annotation (missing) (missing) (missing)

# For testing DiffExprSeq,
conditionList=rel,rel,rem,rem

case2_gene properties (missing) geneCounts (missing) conditions (missing) (missing)

# For testing DiffExprSeq,
level=Gene


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