separate {Fragman}

Separating peaks by a shift window

Description

This function takes a list with positions, heights and weights called "g" and using a shift in base pairs determines when 2 neighboring peaks should be considered only one by getting the tallest peak. For example two peaks found at 173 and 173.5 base pairs are unlikely to be 2 different peaks, therefore only the tallest peak will pe chosen.

Usage

separate(g, shift=1, type="bp")

Arguments

g

List with 3 elements; the information of positions, heights and weights for an individual in certain channel

shift

The number of base pairs to be used for discarding neighboring peaks to the tallest peaks, i.e. if 2 peaks are 0.3 bp together the smalles will be discarded

type

A word indicating if the shift to be used should be used in base pairs or in index. The use is "bp" or "ind"

Details

No major details.

Value

If arguments are correct the function returns a new list containing

$pos

the index positions for the intensities

$hei

the intensities for the fragments found

$wei

the putative weights in base pairs based on the ladder provided

References

Covarrubias-Pazaran G, Diaz-Garcia L, Schlautman B, Salazar W, Zalapa J. Fragman: An R package for fragment analysis. 2016. BMC Genetics 17(62):1-8.

Robert J. Henry. 2013. Molecular Markers in Plants. Wiley-Blackwell. ISBN 978-0-470-95951-0.

Ben Hui Liu. 1998. Statistical Genomics. CRC Press LLC. ISBN 0-8493-3166-8.

Examples

data(my.plants)
x <- big.peaks.col(my.plants[[1]][,1],100)#for any color
#separate(x, shift=1, type="bp") #still needs weight information