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MeapQuantification

Quantify expression data on exon, splicing variant or gene level. Normaliziation has to be done beforehand by 'MeapNormalization'. Processing is run in parallel using the R Message Passing Interface (Rmpi) library to enable faster execution.

It supports Affymetrix GeneChip Exon 1.0 ST and Gene 1.0 ST arrays. This version is build on latest meap library (2.0.0) and Ensembl v70.

Version 2.0
Bundle microarray
Categories Meap
Authors Ping Chen (ping.chen@helsinki.fi)
Issue tracker View/Report issues
Requires R ; meap (R-package)
Source files component.xml MeapQuantification.r
Usage Example with default values

Inputs

Name Type Mandatory Description
normalized CSV Mandatory A CSV file contains a list of paths of all normalized data.
dbConnect CSV Optional Database configuration file stores database connect details. This file is required when generating expression data on 'SpliceVariant' or 'Gene' level.

Outputs

Name Type Description
ExonExpr LogMatrix Exon expression matrix.
SpliceVariantExpr LogMatrix Expression matrix for splicing variants.
GeneExpr LogMatrix Gene expresssion matrix.

Parameters

Name Type Default Description
NProcess int 5 The number of processes are invoked in parallel execution.
annotation string "/opt/sandbox/pchen/MEAPAnnotation_Human_v62" The path of exon array annotation file.
arrayType string "exon" The type of GeneChip array ("exon": GeneChip Exon ST 1.0 array, "gene": GeneChip Gene ST 1.0 array).
cutoff float 0.5 The percentage of transcripts with probes for gene level summarization. If a probe does not map to the number of transcripts defined, the probe will be removed from the summarization. The cutoff value should be 0-1.
exprType string "Exon" A comma-separated string indicating the types of expression matrix to be generated. It can be 'Exon', 'SpliceVariant' or 'Gene'. 'Exon' and 'SpliceVariant' level expression are only for Exon 1.0 ST array. 'Gene' level expression supports both Exon 1.0 ST and Gene 1.0 ST arrays.
filter boolean true Filter transcripts in Ensembl database that do not pass the quality control. The default is 'TRUE'. This parameter is used in generating expression data on 'SpliceVariant' or 'Gene' level.
metaData string (no default) The directory for storing meta data. The meta data will be removed after the execution. It is highly recommend to set this path by user. If empty string is given, the data will be stored in the temporary folder in the execution folder, as given by Anduril.
method string "medianpolish" The summarization method for exon and gene level expression. The default is 'medianpolish'. It can also be 'mean'.
remove boolean false A boolean for removing all meta data. If normalized data are under different folder from the 'metaData', they will be also removed.
version int 70 Ensembl version number.

Test cases

Test case Parameters IN
normalized
IN
dbConnect
OUT
ExonExpr
OUT
SpliceVariantExpr
OUT
GeneExpr
case1 properties normalized dbConnect ExonExpr SpliceVariantExpr GeneExpr

metaData=/tmp,
exprType=Gene


Generated 2018-12-12 07:42:05 by Anduril 2.0.0