armRatioCI

swapChrRegionDfSizeAndMarks

armRatioCI: reads a data.frame and produces AR (arm ratio), CI
(centromeric index) , Guerra and Levan classifications.
swapChrRegionDfSizeAndMarks: reads data.frames to swap arms

size

data.frame

Plot idiograms of karyotypes, plasmids, circular chr. having a set of data.frames for chromosome data and optionally mark data. Two styles of chromosomes can be used: without or with visible chromatids. Supports micrometers, cM and Mb or any unit. Three styles of centromeres are available: triangle, rounded and inProtein; and six styles of marks are available: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow (downArrow), exProtein (inProtein); its legend (label) can be drawn inline or to the right of karyotypes. Idiograms can also be plotted in concentric circles. It is possible to calculate chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x>, karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).

Fernando Roa

idiogramFISH

Shiny App. Idiograms with Marks and Karyotype Indices

Mariana PC Telles 

armRatioCI function

<dl><dt>dfChrSize</dt>
<dd>name of data.frame with columns: shortArmSize, longArmSize</dd>
<dt>rnumeric</dt>
<dd>boolean, returns only numeric AR, CI</dd>
<dt>dfMarkPos</dt>
<dd>name of data.frame of marks</dd>
<dt>chrNamesToSwap</dt>
<dd>name of chr. names to swap arms</dd></dl>

Arguments

FUNCTIONS armRatioCI and swapChrRegionDfSizeAndMarks. — armRatioCI

<dl>

<dt>dfChrSize</dt>
<dd>name of data.frame with columns: shortArmSize, longArmSize</dd>


<dt>rnumeric</dt>
<dd>boolean, returns only numeric AR, CI</dd>


<dt>dfMarkPos</dt>
<dd>name of data.frame of marks</dd>


<dt>chrNamesToSwap</dt>
<dd>name of chr. names to swap arms</dd>

</dl>

armRatioCI: FUNCTIONS armRatioCI and swapChrRegionDfSizeAndMarks.

Description

Usage

Value

Arguments

References

See Also

Examples