calculates fraction (%) of chromosome for each mark
perMark(dfMarkPos, listOfdfChromSize, result = "list", bToRemove = "")data.frame, of marks' position
list of data.frames or data.frame of chr. sizes.
character, type of return, "data.frame" or "list"
character vector, bands to ignore
list
load(system.file("shinyApps", "iBoard/www/rda/monoholoCS.rda", package = "idiogramFISH"))
load(system.file("shinyApps", "iBoard/www/rda/monoholoMarks.rda", package = "idiogramFISH"))
monoholoMarks2 <- fillMarkInfo(monoholoMarks, monoholoCS)
#>
#> Checking columns from listOfdfChromSize
#>
#> Checking mandatory columns from listOfdfChromSize for chr. with cen.:
#>
#> chrName, shortArmSize,longArmSize,
#> (column OTU is necessary if more than one species)
#>
#> OTU Species mono has all columns with info to have monocen. If not, you have to clean your data
#>
#> Checking columns from listOfdfChromSize
#>
#> Checking mandatory columns from listOfdfChromSize for chr. without cen.:
#>
#> chrName, chrSize,
#> (column OTU is necessary if more than one species)
#>
#> OTU Species holo has all columns with info to have holocen. If not, you have to clean your data
#>
#> Checking mandatory columns from dfMarkPos: chrName, markName, chrRegion,markDistCen
#>
#> (column OTU is necessary if more than one species)
#> markSize can be absent when cM style
#>
#> Checking mandatory columns from dfMarkPos (without cen.): chrName, markName, markPos
#>
#> (column OTU is necessary if more than one species)
#> markSize column is not necessary for style of mark cM
#>
#> OK marks of OTU Species holo checked
#>
#> Checking mandatory columns from dfCenMarks: chrName, markName
#> (column OTU is necessary if more than one species)
#>
#> OK cen. marks of OTU Species mono checked
#>
#> Comparing chromosome names among data.frames:
#>
#> Comparing OTU named: Species mono of main data.frame with correspondent data.frame parlistOfdfMarkPosMonocen
#>
#> No divergence
#>
#> Comparing chromosome names among data.frames:
#>
#> Comparing OTU named: Species holo of main data.frame with correspondent data.frame parlistOfdfMarkPosHolocen
#>
#> No divergence
#>
#> Comparing chromosome names among data.frames:
#>
#> Comparing OTU named: Species mono of main data.frame with correspondent data.frame parlistOfdfMarkPosDataCen
#>
#> No divergence
perMark(monoholoMarks2, monoholoCS, result = "data.frame")
#>
#> Calculating position of each mark in terms of % of chromosome
#> mark's style 'cen' does not have size, no % calculated, see ruler
#> OTU markName 1 2 3 4 X
#> 1 Species holo chrSize 3.0000000 4.000 2.00 5.0 NA
#> 2 Species holo 45S 0.5000000 NA NA NA NA
#> 3 Species holo 45S_per 0.1666667 NA NA NA NA
#> 4 Species holo 5S NA NA 0.50 0.5 NA
#> 5 Species holo 5S_per NA NA 0.25 0.1 NA
#> 6 Species holo CMA NA NA NA 0.5 NA
#> 7 Species holo CMA_per NA NA NA 0.1 NA
#> 8 Species holo DAPI NA 0.500 0.50 NA NA
#> 9 Species holo DAPI_per NA 0.125 0.25 NA NA
#> 10 Species mono chrSize 7.0000000 9.000 5.00 NA 3.0000000
#> 11 Species mono 45S 1.0000000 NA NA NA 1.0000000
#> 12 Species mono 45S_per 0.1428571 NA NA NA 0.3333333
#> 13 Species mono 5S 0.7000000 NA NA NA NA
#> 14 Species mono 5S_per 0.1000000 NA NA NA NA
#> 15 Species mono DAPI NA NA 1.00 NA NA
#> 16 Species mono DAPI_per NA NA 0.20 NA NA