calculates position of marks in fraction of (%) chromosome units (0-1)
posCalc(
dfMarkPos,
listOfdfChromSize,
bToRemove = "",
markDistType = "beg",
origin = "b",
showBandList = FALSE,
result = "tibble"
)
fillMarkInfo2(dfMarkPos, dfChrSize)
fillMarkInfo(dfMarkPos, dfChrSize, markDistType = "beg", origin = "b")data.frame of marks' position
list (for posCalc) or data.frames of chr. sizes.
character, bands to remove from calc. of pos.
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)
character, 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.
boolean, show row of all bands in tibble, see "result"
character, use "tibble" to get results in tibble, "data.frame", or other string results in a list
data.frame of chr. sizes
list, tibble
data.frame of marks
data.frame of marks
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
posCalc(monoholoMarks2, monoholoCS, result = "data.frame")
#> # A tibble: 12 × 7
#> OTU markName `1` `2` `3` `4` X
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Species holo 45S 0.167 NA NA NA NA
#> 2 Species holo 5S NA NA 0.25 NA NA
#> 3 Species holo 5S NA NA NA 0.8 NA
#> 4 Species holo CMA NA NA NA 0.5 NA
#> 5 Species holo DAPI NA 0.375 NA NA NA
#> 6 Species holo DAPI NA NA 0 NA NA
#> 7 Species mono 45S 0.5 NA NA NA NA
#> 8 Species mono 45S NA NA NA NA 0
#> 9 Species mono 5S 0.257 NA NA NA NA
#> 10 Species mono CMA NA NA NA NA 0.333
#> 11 Species mono DAPI 0.429 NA NA NA NA
#> 12 Species mono DAPI NA NA 0.6 NA NA