14 Datasets
14.1 Chr. basic data Holo.
dfChrSizeHolo
: Example data for holocentrics for 1 species
bigdfChrSizeHolo
: Example data for holocentrics for several species, OTU
parentalAndHybHoloChrSize
: Example data for holocentrics for several species, OTU
bigdfOfChrSize3Mb
: Example data in Mb without chr. arms for three species, OTU
Format
data.frame with columns:
OTU
grouping OTU (species), optional if only one OTU
chrName
name of chromosome
chrSize
size of chromosome, micrometers or Mb
group
chromosome group, optional
chrNameUp
optional name over kar.
Mbp
optional name to show size in Mbp under kar., use only when chrSize is not in Mbp. To be used with chrSizeMbp=TRUE
14.2 Chr. basic data Monocen.
dfOfChrSize
: Example data for monocentrics
bigdfOfChrSize
: Example data for monocentrics for several species, OTU
humChr
: Data for human karyotype, measured from Adler (1994)
allChrSizeSample
: Example data for monocentrics for several species, OTU
parentalAndHybChrSize
: Example data for monocentrics for GISH
traspadf
: Example data for Tradescantia (Rhoeo) spathacea (Golczyk et al., 2005)
Format
data.frame with columns:
OTU
species, optional if only one OTU (species)
chrName
name of chromosome
shortArmSize
size of short arm, micrometers
longArmSize
size of long arm, micrometers
group
chr group, optional
chrNameUp
optional name over kar.
Mbp
optional name to show size in Mbp, use only when shortArmSize is not in Mbp
14.3 Mark characteristics
Source: R/dfMarkStyle.R
style
column does not apply to cen. marks, only color.
dfMarkColor
: Example General data for marks NOT position
humMarkColor
: human bands’ characteristics, from Adler (1994)
mydfMaColor
: mark characteristics used in vignette of phylogeny
14.4 Mark Positional data - Holocen.
Source: R/markdataholo.R
bigdfMarkPosHolo
: Example data for mark position of holocentrics with column OTU
dfMarkPosHolo
: Example data for mark position of holocentrics
dfAlloParentMarksHolo
: Example data for mark position of GISH
bigdfOfMarks3Mb
: Example data for mark position in Mb
14.5 Mark Positional data - monocentrics
Source: R/markposDFs.R
bigdfOfMarks
: Example data for mark position with column OTU
dfOfMarks
: Example data for marks’ position
dfOfMarks2
: Marks’ position including cen. marks
humMarkPos
: human karyotype bands’ (marks) positions, measured from Adler (1994)
allMarksSample
: Example data for marks’ position
dfAlloParentMarks
: Example data for mark position of GISH of monocen.
traspaMarks
: T. spathacea (Rhoeo) marks’ positions, from Golczyk et al. (2005)
Format
bigdfOfMarks a data.frame with columns:
OTU
OTU, species, mandatory if in dfChrSize
chrName
name of chromosome
markName
name of mark
chrRegion
use p for short arm, q for long arm, and cen for centromeric
markDistCen
distance of mark to centromere (not for cen)
markSize
size of mark (not for cen)
14.6 File eightSpIqtree.treefile
See chapter phylogeny (Nguyen et al., 2015)
14.7 File revBayesTutorial.tree
See chapter phylogeny (Höhna et al., 2017)