junctionDUreport: Differential junction usage estimation

Description Usage Arguments Value Author(s) See Also Examples

Description

Estimate differential usage at junction level. When targets has only two conditions, and contrast is not set, the estimation of differential expression and usage is done with an exact test, otherwise is estimated using a generalized linear model.

Usage

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  junctionDUreport( counts, 
                    targets,
                    appendTo = NULL, 
                    minGenReads = 10, 
                    minRds = 0.05,
                    threshold = 5,
                    offset = FALSE, 
                    offsetUseFitGeneX = TRUE,
                    contrast = NULL, 
                    forceGLM = FALSE)

Arguments

counts

An object of class ASpliCounts

targets

A dataframe containing sample, bam and experimental factor columns.

appendTo

An object of class ASpliDU to which append the results of junction differential usage. If appendTo is NULL a new ASpliDU is created

minGenReads

Junctions within genes with at least an average of minGenReads reads for all conditions are included into the differential junction usage test. Default value is 10 reads.

minRds

Junctions within genes with at least an average of minRds read density for all conditions are included into the differential bin usage test. Junctions with at least an average of minRds read density for any condition are included into the differential junction usage test. Default value is 0.05.

threshold

Junction with at least threshold counts are included into the differential usage test.

offset

Corrects junction counts using an offset matrix derived from gene expression data. Default = FALSE

offsetUseFitGeneX

Fit a GLM using gene counts to build the offset matrix. This argument is used only when 'offset' argument is set to TRUE. The default value is TRUE

contrast

Define the comparison between conditions to be tested. contrast should be a vector with length equal to the number of experimental conditions defined by targets. The values of this vector are the coefficients that will be used to weight each condition, the order of the values corresponds to the order given by getConditions function. When contrast is NULL, defaults to a vector containing -1, as the first value, 1 as the second an zero for all the remaining values, this corresponds to a pair comparison where the first condition is assumed to be a control and the second condition is the treatment, all other conditions are ignored. Default = NULL

forceGLM

Force the use of a generalized linear model to estimate differential expression and usage. Default = FALSE

Value

An ASpliDU object with results of differential usage of junctions

Author(s)

Estefania Mancini, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz

See Also

edgeR, DUreport Accessors: junctionsDU Export: writeDU

Examples

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	#This function has been deprecated. Please see vignette for new pipeline.

chernolab/ASpli documentation built on March 11, 2021, 12:24 a.m.