Up: Component summary Function

ExprTableReport

Generates expression statistics into an HTML report. All heatmaps use gene names, so they need to be provided either in a GTF file or as part of the expression matrix. The annotation file can be used also to subset the genes of interest, only genes included in the annotation file will be used for the statistics and plots.

Version 1.0
Bundle sequencing
Categories Expression
Authors Alejandra Cervera (alejandra.cervera@helsinki.fi), Katherine Icay (katherine.icay@helsinki.fi), Julia Casado (julia.casado@helsinki.fi)
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Source files component.xml function.scala
Usage Example with default values

Inputs

Name Type Mandatory Description
expr CSV Mandatory Expression matrix. Values should be in log2 if visualization is enabled.
ref CSV Mandatory CSV file containing sample names and treatment groups. Sample names must match column names of expr.
colLabels CSV Optional Label heatmaps with, i.e. clinical information.
annotation GTF Optional Ensembl GTF annotation file to be used for grouping genes in biotypes.
geneSet CSV Optional One-column list of interesting genes (Ensembl geneId) to create heatmap for. If empty, the oncogenes from the cancer census list will be used.
bodyMap CSV Optional Index matrix of geneIds (rows) per tissue (columns). If empty, the Illumina Body Map will be used.

Outputs

Name Type Description
table CSV
expressed CSV Expression table that has at least one column with the gene or transcript ids, and expression columns corresponding to several samples with the expression values in log2.
document Latex Document containing all the visuals produced.
report HTML Expression statistics report.

Parameters

Name Type Default Description
bodySite string "body" Any body tissue from the Illumina Body Map, can be the emtpy string or heart, stomach, brain ...
keyCol string "gene_id" Column name with the unique ids to be used.
minimum float 0 Threshold for minimum expression to be included in the reduced CSV output.
nameCol string "gene_name" When input annotation is not provided, then the column containing gene names must be defined from expr.
sampleKeyCol string "Key" Column name for sample IDs in input CSV ref.
top int 10 Number of top genes to be reported.

Test cases

Test case Parameters IN
expr
IN
ref
IN
colLabels
IN
annotation
IN
geneSet
IN
bodyMap
OUT
table
OUT
expressed
OUT
document
OUT
report
case1 (missing) expr ref (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing)

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