Component: MeapQuantification

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 MeapQuantification( normalized = CSV, //dbConnect = CSV, NProcess = 5, annotation = "/opt/sandbox/pchen/MEAPAnnotation_Human_v62", arrayType = "exon", cutoff = 0.5, exprType = "Exon", filter = true, metaData = <string>, method = "medianpolish", remove = false, version = 70 )

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.

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.

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.

Name

Type

Default

Description

NProcess

int

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

Ensembl version number.

Test cases