armRatioCI: reads a data.frame and produces AR (arm ratio), CI (centromeric index) , Guerra and Levan classifications.
swapChrRegionDfSizeAndMarks: reads data.frames to swap arms
armRatioCI(dfChrSize, rnumeric = FALSE)
swapChrRegionDfSizeAndMarks(dfChrSize, dfMarkPos, chrNamesToSwap)name of data.frame with columns: shortArmSize, longArmSize
boolean, returns only numeric AR, CI
name of data.frame of marks
name of chr. names to swap arms
data.frame (armRatioCI)
list of data.frames (swapChrRegionDfSizeAndMarks)
LEVAN A, FREDGA K, SANDBERG AA (1964) NOMENCLATURE FOR CENTROMERIC POSITION ON CHROMOSOMES. Hereditas 52:201-220.
Guerra. 1986. Reviewing the chromosome nomenclature of Levan et al. Braz. Jour. Gen. Vol IX, 4, 741-743
armRatioCI(dfOfChrSize)
#> chrName shortArmSize longArmSize smallest largest chrSize AR CI ARnum
#> 1 1 3 4 3 4 7 1.3 42.9 1.3
#> 2 2 4 5 4 5 9 1.2 44.4 1.2
#> 3 3 2 3 2 3 5 1.5 40.0 1.5
#> 4 X 1 2 1 2 3 2.0 33.3 2.0
#> CInum Guerra Levan
#> 1 42.9 M m
#> 2 44.4 M m
#> 3 40.0 SM m
#> 4 33.3 SM sm
armRatioCI(bigdfOfChrSize)
#>
#> Calculating chromosome indexes in Species 1
#> Calculating chromosome indexes in Species 2
#> Calculating chromosome indexes in Species 3
#> Calculating chromosome indexes in Species 4
#> Calculating chromosome indexes in Species 5
#> Calculating chromosome indexes in Species 6
#> Calculating chromosome indexes in Species 7
#> Calculating chromosome indexes in Species 8
#> Calculating chromosome indexes in Species 9
#> OTU chrName shortArmSize longArmSize smallest largest chrSize AR
#> 1 Species 1 1 1.5 2.0 1.5 2.0 3.5 1.3
#> 2 Species 1 2 2.0 2.5 2.0 2.5 4.5 1.2
#> 3 Species 1 3 1.0 2.0 1.0 2.0 3.0 2.0
#> 4 Species 2 1 3.0 4.0 3.0 4.0 7.0 1.3
#> 5 Species 2 2 4.0 5.0 4.0 5.0 9.0 1.2
#> 6 Species 2 3 2.0 3.0 2.0 3.0 5.0 1.5
#> 7 Species 2 X 1.0 2.0 1.0 2.0 3.0 2.0
#> 8 Species 2 4 3.0 4.0 3.0 4.0 7.0 1.3
#> 9 Species 3 1 3.2 4.0 3.2 4.0 7.2 1.2
#> 10 Species 3 2 4.5 5.0 4.5 5.0 9.5 1.1
#> 11 Species 3 3 2.0 3.0 2.0 3.0 5.0 1.5
#> 12 Species 3 4 1.5 2.0 1.5 2.0 3.5 1.3
#> 13 Species 3 5 4.8 6.0 4.8 6.0 10.8 1.2
#> 14 Species 3 6 6.1 7.0 6.1 7.0 13.1 1.1
#> 15 Species 4 1 1.5 2.0 1.5 2.0 3.5 1.3
#> 16 Species 4 2 2.0 2.5 2.0 2.5 4.5 1.2
#> 17 Species 4 3 1.0 1.5 1.0 1.5 2.5 1.5
#> 18 Species 5 1 3.0 4.0 3.0 4.0 7.0 1.3
#> 19 Species 5 2 4.0 5.0 4.0 5.0 9.0 1.2
#> 20 Species 5 3 2.0 3.0 2.0 3.0 5.0 1.5
#> 21 Species 5 X 1.0 2.0 1.0 2.0 3.0 2.0
#> 22 Species 5 4 3.0 4.0 3.0 4.0 7.0 1.3
#> 23 Species 6 1 3.2 4.0 3.2 4.0 7.2 1.2
#> 24 Species 6 2 4.5 5.0 4.5 5.0 9.5 1.1
#> 25 Species 6 3 2.0 3.0 2.0 3.0 5.0 1.5
#> 26 Species 6 4 1.5 2.0 1.5 2.0 3.5 1.3
#> 27 Species 6 5 4.8 6.0 4.8 6.0 10.8 1.2
#> 28 Species 6 6 6.1 7.0 6.1 7.0 13.1 1.1
#> 231 Species 7 1 3.9 4.0 3.9 4.0 7.9 1.0
#> 241 Species 7 2 3.8 4.0 3.8 4.0 7.8 1.1
#> 251 Species 7 3 3.7 4.0 3.7 4.0 7.7 1.1
#> 261 Species 7 4 3.8 4.1 3.8 4.1 7.9 1.1
#> 271 Species 7 5 3.9 3.9 3.9 3.9 7.8 1.0
#> 281 Species 7 6 3.9 4.0 3.9 4.0 7.9 1.0
#> 232 Species 8 1 0.9 8.0 0.9 8.0 8.9 8.9
#> 242 Species 8 2 0.8 8.0 0.8 8.0 8.8 10.0
#> 252 Species 8 3 0.7 8.0 0.7 8.0 8.7 11.4
#> 262 Species 8 4 0.8 8.2 0.8 8.2 9.0 10.2
#> 272 Species 8 5 0.9 7.8 0.9 7.8 8.7 8.7
#> 282 Species 8 6 0.9 8.0 0.9 8.0 8.9 8.9
#> 233 Species 9 1 0.4 4.0 0.4 4.0 4.4 10.0
#> 243 Species 9 2 0.5 5.0 0.5 5.0 5.5 10.0
#> 253 Species 9 3 0.6 6.0 0.6 6.0 6.6 10.0
#> 263 Species 9 4 0.8 8.0 0.8 8.0 8.8 10.0
#> 273 Species 9 5 0.9 9.0 0.9 9.0 9.9 10.0
#> 234 Species 9 1 0.2 2.0 0.2 2.0 2.2 10.0
#> 244 Species 9 2 0.4 4.0 0.4 4.0 4.4 10.0
#> 254 Species 9 3 0.6 6.0 0.6 6.0 6.6 10.0
#> 264 Species 9 4 0.8 8.0 0.8 8.0 8.8 10.0
#> 274 Species 9 5 10.0 10.0 10.0 10.0 20.0 1.0
#> CI ARnum CInum Guerra Levan
#> 1 42.9 1.3 42.9 M m
#> 2 44.4 1.2 44.4 M m
#> 3 33.3 2.0 33.3 SM sm
#> 4 42.9 1.3 42.9 M m
#> 5 44.4 1.2 44.4 M m
#> 6 40.0 1.5 40.0 SM m
#> 7 33.3 2.0 33.3 SM sm
#> 8 42.9 1.3 42.9 M m
#> 9 44.4 1.2 44.4 M m
#> 10 47.4 1.1 47.4 M m
#> 11 40.0 1.5 40.0 SM m
#> 12 42.9 1.3 42.9 M m
#> 13 44.4 1.2 44.4 M m
#> 14 46.6 1.1 46.6 M m
#> 15 42.9 1.3 42.9 M m
#> 16 44.4 1.2 44.4 M m
#> 17 40.0 1.5 40.0 SM m
#> 18 42.9 1.3 42.9 M m
#> 19 44.4 1.2 44.4 M m
#> 20 40.0 1.5 40.0 SM m
#> 21 33.3 2.0 33.3 SM sm
#> 22 42.9 1.3 42.9 M m
#> 23 44.4 1.2 44.4 M m
#> 24 47.4 1.1 47.4 M m
#> 25 40.0 1.5 40.0 SM m
#> 26 42.9 1.3 42.9 M m
#> 27 44.4 1.2 44.4 M m
#> 28 46.6 1.1 46.6 M m
#> 231 49.4 1.0 49.4 M M
#> 241 48.7 1.1 48.7 M m
#> 251 48.1 1.1 48.1 M m
#> 261 48.1 1.1 48.1 M m
#> 271 50.0 1.0 50.0 M M
#> 281 49.4 1.0 49.4 M M
#> 232 10.1 8.9 10.1 A t
#> 242 9.1 10.0 9.1 A t
#> 252 8.0 11.4 8.0 A t
#> 262 8.9 10.2 8.9 A t
#> 272 10.3 8.7 10.3 A t
#> 282 10.1 8.9 10.1 A t
#> 233 9.1 10.0 9.1 A t
#> 243 9.1 10.0 9.1 A t
#> 253 9.1 10.0 9.1 A t
#> 263 9.1 10.0 9.1 A t
#> 273 9.1 10.0 9.1 A t
#> 234 9.1 10.0 9.1 A t
#> 244 9.1 10.0 9.1 A t
#> 254 9.1 10.0 9.1 A t
#> 264 9.1 10.0 9.1 A t
#> 274 50.0 1.0 50.0 M M
swapChrRegionDfSizeAndMarks(dfOfChrSize, dfOfMarks, "1")
#> $dfChrSize
#> chrName shortArmSize longArmSize
#> 1 1 4 3
#> 2 2 4 5
#> 3 3 2 3
#> 4 X 1 2
#>
#> $dfMarkPos
#> chrName markName chrRegion markSize markDistCen
#> 1 1 5S q 1 0.5
#> 2 1 45S p 1 0.5
#> 3 X 45S p 1 1.0
#> 4 3 DAPI q 1 1.0
#>