Duplication rate ~ total read count fit model

duprateExpDensPlot Duplication rate ~ total read count fit model

duprateExpFit(DupMat)

Arguments

DupMat

The duplication matrix calculated by analyzeDuprates

Value

The GLM and the coefficients of the fitted logit function

Details

Fit a Generalized Linear Model using a logit function between thegene duplication rate and the total read count.

Examples

# dm is a duplication matrix calculated by analyzeDuprates:
# R> dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads)
attach(dupRadar_examples)
#> The following objects are masked from dupRadar_examples (pos = 3):
#> 
#>     dm, dm.bad
#> The following objects are masked from dupRadar_examples (pos = 4):
#> 
#>     dm, dm.bad
#> The following objects are masked from dupRadar_examples (pos = 5):
#> 
#>     dm, dm.bad

# duprate plot
duprateExpFit(DupMat=dm)
#> $glm
#> 
#> Call:  glm(formula = y ~ x, family = binomial(link = "logit"))
#> 
#> Coefficients:
#> (Intercept)            x  
#>      -3.200        1.159  
#> 
#> Degrees of Freedom: 16568 Total (i.e. Null);  16567 Residual
#>   (6659 observations deleted due to missingness)
#> Null Deviance:	    4684 
#> Residual Deviance: 1481 	AIC: 10240
#> 
#> $intercept
#> (Intercept) 
#>  0.04075061 
#> 
#> $slope
#>        x 
#> 3.186793 
#>