idiogramFISH (version 2.0.0)

posCalc: FUNCTION posCalc

Description

calculates position of marks in fraction of (%) chromosome units (0-1)

Usage

posCalc(
  dfMarkPos,
  listOfdfChromSize,
  bToRemove = "",
  markDistType = "beg",
  origin = "b",
  result = "tibble"
)

Arguments

dfMarkPos

data.frame of marks' position

listOfdfChromSize

list data.frames of chr. sizes. Require col. chrSize for all. Use armRatioCI

bToRemove,

character, bands to remove from calc. of pos.

markDistType

markDistType character, if "cen" = the distance you provided in data.frame (dfMarkPos) column markDistCen or markPos is to the center of the mark, if "beg" = the distance you provided is to the beginning of the mark (Default)

origin,

For non-monocentric chr. (for holocentrics only) Use "b" (default) if distance to mark in ("markPos" column in "dfMarkPos") data.frame measured from bottom of chromosome, use "t" for distance to mark from top of chr.

result

character, use "tibble" to get results in tibble, other string results in a list

Value

list, tibble

Examples

# NOT RUN {
# Monocentrics - Beginning with two data.frames with column OTU
require(idiogramFISH)

dfOfChrSize$OTU<-1
dfOfMarks2$OTU<-1

# check missing data

dfOfMarks2[which(is.na(dfOfMarks2$markSize) & dfOfMarks2$chrRegion %in% c("p","q") ),]
# markSize and markDistCen missing

# add markDistCen
dfOfMarks2$markDistCen <- ifelse( is.na(dfOfMarks2$markDistCen) &
dfOfMarks2$chrRegion %in% c("p","q"),
0,
dfOfMarks2$markDistCen)

# add markSize
XshortSize <- dfOfChrSize[which(dfOfChrSize$chrName=="X"),]$shortArmSize
dfOfMarks2[which(dfOfMarks2$chrName=="X" & dfOfMarks2$chrRegion=="p")  ,]$markSize<-XshortSize

# add column chrSize if missing
dfOfChrSizeWithChrSize <- armRatioCI(dfOfChrSize)

# data.frame of chr. size to list
listOfdfChr <- idiogramFISH:::dfToListColumn(dfOfChrSizeWithChrSize)

ti<-posCalc(dfOfMarks2,listOfdfChr)
as.list(ti[[1]][,1])
posCalc(dfOfMarks2,listOfdfChr, result="list")

# holocentrics example

dfChrSizeHolo$OTU<-2
dfMarkPosHolo$OTU<-2

# data.frame of chr. size to list
listOfdfChrHolo <- idiogramFISH:::dfToListColumn(dfChrSizeHolo)

ti2<-posCalc(dfMarkPosHolo,listOfdfChrHolo)
ti2

posCalc(dfMarkPosHolo,listOfdfChrHolo, result="list")

as.list(ti2[[1]][,1] )

# }