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GlobalCorrelation

Compute correlation between miRNA and gene/transcript expression.

Version 1.2
Bundle sequencing
Categories smallRNA Expression Integration
Authors Ping Chen (ping.chen@helsinki.fi), Katherine Icay (katherine.icay@helsinki.fi)
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Requires R
Source files component.xml GlobalCorrelation.R
Usage Example with default values

Inputs

Name Type Mandatory Description
gene CSV Mandatory Gene expression matrix.
mirna CSV Mandatory miRNA expression matrix.

Outputs

Name Type Description
correlated_filtered CSV CSV file containing correlated miRNA-mRNA pairs within cutoff values and with minSample.
correlated_all CSV CSV file containing all correlated miRNA-mRNA pairs with minSample.
expression_miRNA CSV Filtered expression matrix of miRNAs in correlated_filtered.
expression_mRNA CSV Filtered expression matrix of mRNAs in correlated_filtered.

Parameters

Name Type Default Description
cutoff float 0.4 The absolute threshold defining the most interesting miRNA-mRNA pairs. If cutoffType="correlation", both positively and negatively correlated pairs will appear. If pvalue is chosen, only those values less than or equal to the cutoff will apear.
cutoffType string "correlation" The type of cutoff. Values are either correlation (corr) or pavalue (pval).
hasNA boolean false A boolean defines if there is missing value in the input expression data.
method string "pearson" a character string indicating which correlation coefficient (or covariance) is to be computed. One of pearson (default), kendall, or spearman, can be abbreviated.
minSample int 1 The minimum number of samples. Samples with missing values will be removed when computing correlation. It defines the minimum number of samples required for correlation analysis.

Test cases

Test case Parameters IN
gene
IN
mirna
OUT
correlated_filtered
OUT
correlated_all
OUT
expression_miRNA
OUT
expression_mRNA
case1 (missing) gene mirna correlated_filtered correlated_all expression_miRNA expression_mRNA

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