entropy.pos: Entropy at a position
In egking/DSPRqtl: Analysis of DSPR phenotypes in R

Description Usage Arguments Value Author(s) References

entropy.pos calculates the entropy (proportion of missing information) at a given position.

1	entropy.pos(peakChr, peakPos, design, phenotype.dat, id.col, sex)

`peakChr`	character vector of length one. Must be one of the major chromosome arms in the Drosophila genome ('X','2L','2R','3L',or '3R').
`peakPos`	numeric vector of length one. A position in base pairs in the DSPR position list (every 10kb).
`design`	a character string. For inbred RIL designs: 'inbredA', 'inbredB'. For cross designs: AAcross, BBcross, or 'ABcross'. A and B refer to the pA and pB set of DSPR RILs.
`phenotype.dat`	`data.frame` containing phenotype data. For inbred designs, there must be a column of numeric RIL ids (must be named patRIL). For the ABcross design, there must be both a patRIL and matRIL column specifying the pA and pB RIL ids. Cross designs also require a sex column for correct specification of the genotypes on the X chromosome.
`id.col`	a character string identifying the name of the column containing unique ids for the samples. e.g. for an inbred design, the patRIL column can be used as the id.
`sex`	a character string (either 'm' or 'f') specifying the sex of the measured individuals. This argument must be supplied for the AB cross design for correct specification of the genotypes on the X chromosome.

A numeric vector: the entropy at the given position for the set of RILs in the phenotype.dat data.frame. In the case of the ABcross, the A and B entropy are calculated separately and both are returned.

Elizabeth King (kingeg@missouri.edu)

Shannon, C.E. 1984. A mathematical theory of communication. Bell System Technical Journal 27(3): 379-423. http://en.wikipedia.org/wiki/Information_theory#Entropy

egking/DSPRqtl documentation built on May 16, 2019, 12:14 a.m.