Description Objects from the Class Slots Methods Author(s) See Also Examples

Results from scanning the genome with the inversion model for trial segments of fixed window size.

`scan`

objects are typically generated by callings to the constructor function `scanInv`

`leftBP`

:Object of class

`"matrix"`

Left brake-point coordinates (right SNP)`rightBP`

:Object of class

`"matrix"`

Right brake-point coordinates (right SNP)`leftBP2`

:Object of class

`"matrix"`

Left brake-point coordinates (left SNP)`rightBP2`

:Object of class

`"matrix"`

Right brake-point coordinates (right SNP)`LogLike`

:Object of class

`"matrix"`

Log-likelihood ratio for each trial segment`prob`

:Object of class

`"matrix"`

probability of no-inversion for each trial segment`ent`

:Object of class

`"matrix"`

entropy for each trial segment`entTh`

:Object of class

`"matrix"`

entropy threshold for each trial segment`bic`

:Object of class

`"matrix"`

BIC for each trial segment`window`

:Object of class

`"numeric"`

window size

- getInv
`signature(object = "scan")`

: gets scan results into a matrix- getROIs
`signature(object = "scan")`

: get regions of interest, overlapping trial segments with significant BIC- listInv
`signature(object = "scan")`

: determines the inversion sequence for each ROI- plot
`signature(x = "scan")`

: plots`scan`

results, set option`which=c("bic","log","prob","ent")`

to plot BIC, log-likelihood ratio, probability of no inversion or entropy; and`thBic=0`

to plot segments with BIC greater than 0- show
`signature(object = "scan")`

: shows scan results for each ROI

Alejandro Caceres acaceres@creal.cat

`listInv`

, `HaploCode`

, `getInv`

, `getROIs`

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