idiogramFISH (version 1.15.3)

citrusSize: FUNCTIONS: citrusSize, citrusMarkPos, markOverCMA

Description

Helper function to create data.frames with chr. size and mark size data for Citrus based on categories in Carvalho et al. (2005)

Usage

citrusSize(
  A = 0,
  B = 0,
  C = 0,
  D = 0,
  E = 0,
  F = 0,
  FL = 0,
  FL0 = 0,
  G = 0,
  shortArm = 1.2,
  longArm = 1.7,
  shortArmFL = 1.3,
  longArmFL = 1.8,
  OTU = "OTU 1"
)
citrusMarkPos(
  chrSizeDf,
  mSizePter = 0.25,
  mSizeQter = 0.35,
  mSizePprox = 0.35,
  mOther = 0.25,
  markName = "CMA"
)
markOverCMA(
  citrusMarkPosDF,
  chrType = "B",
  chrName,
  chrRegion = "p",
  markName = "45S"
)

Arguments

A

number of A to calculate (citrusSize)

B

number of B to calculate (citrusSize)

C

number of C to calculate (citrusSize)

D

number of D to calculate (citrusSize)

E

number of E to calculate (citrusSize)

F

number of F to calculate (citrusSize)

FL

number of FL to calculate (citrusSize)

FL0

number of FL0 to calculate (citrusSize)

G

number of G to calculate (citrusSize)

shortArm

for A to G (not FL) (citrusSize)

longArm

for A to G (not FL) (citrusSize)

shortArmFL

for FL (citrusSize)

longArmFL

for FL (citrusSize)

OTU

name of species (citrusSize)

chrSizeDf

data.frame created with citrusSize function (citrusMarkPos)

mSizePter

numeric, default size for P(short) ter (terminal) bands. 0.25 (default) (citrusMarkPos)

mSizeQter

numeric, default size for Q(long) ter (terminal) bands. 0.35 (default) (citrusMarkPos)

mSizePprox

numeric, default size for P prox (proximal) bands. 0.35 (default) (citrusMarkPos)

mOther

numeric, default size for other bands. 0.25 (default) (citrusMarkPos)

markName

character, default name of mark "CMA", or "45S", respectively. (citrusMarkPos,markOverCMA)

citrusMarkPosDF

data.frame, with CMA marks (markOverCMA)

chrType

character, defaults to "B", chr. type to duplicate mark (markOverCMA)

chrName

character, defaults to "B", chr. name to duplicate mark (markOverCMA)

chrRegion

character, arm, defaults to "p". for mark duplication (markOverCMA)

Value

data.frame

data.frame

data.frame

References

Carvalho, R., Soares Filho, W. S., Brasileiro-Vidal, A. C., & Guerra, M. (2005). The relationships among lemons, limes and citron: A chromosomal comparison. Cytogenetic and Genome Research, 109(1<U+2013>3), 276<U+2013>282. https://doi.org/10.1159/000082410

Examples

# NOT RUN {
citrusSizeDF <- citrusSize(B=1,D=11,F=4,FL0=2,OTU="C. jambhiri")

citrusMarkPosDF <- citrusMarkPos(citrusSizeDF)
citrusMarkPosDF45S<-markOverCMA(citrusMarkPosDF, chrType="B", chrRegion="p", markName="45S")
# }