Initial commit of read.cross.tidy()

[aaronwolen]

Hi Karl,

This PR adds support for a new read.cross() format I'm calling "tidy" because genotype, phenotype and map data are stored in separate files using a standard data.frame-like format:

Phenotypes:

	1	2	3	4	5
T264	118.3	264	194.9	264	145.4

Genotypes:

	1	2	3	4	5
D10M44	B	-	-	B	H
D1M3	B	B	H	B	H
D1M75	B	B	H	H	H
D1M215	H	B	H	H	H
D1M309	H	H	H	H	B

Map:

	chr	cm
D10M44	1	0
D1M3	1	0.996
D1M75	1	24.85
D1M215	1	40.41
D1M309	1	49.99

The advantage of this format is each file can be easily loaded into R with read.table() for analysis/visualization outside of R/qtl. For projects using R/qtl I usually maintain two sets of genotype/phenotype files: 1 for general analysis and 1 set formatted for R/qtl. Adding something like read.cross.tidy() would allow me to avoid that redundancy, so that's my selfish motivation behind this PR.

I'd call it draft code at this point; it works but lacks the extensive data checks found in the other read.cross.*() functions. I can bring it up to parity but wanted to gauge your level interest before proceeding.

[kbroman]

Great idea! I'll merge it into the devel branch. I'm reserving the master branch for the latest release.

[aaronwolen]

Cool! I'll integrate it with read.cross() and add some of the missing data checks. Let me know if you have any other suggestions.

[aaronwolen]

I made some improvements to the original PR:

• added write.cross.tidy()
• added "tidy" support to read.cross() and write.cross()
• NA columns are inserted for individuals missing in the genotype or phenotype files

I wrote a few simple tests to ensure a cross created with read.cross.tidy() is identical to one created with an existing read.cross.*() function and verify that cross data can be round tripped:

files -> `read.cross.tidy()` -> `write.cross.tidy()` -> files -> `read.cross.tidy()`

I didn't want to muck up your existing testing infrastructure so I kept my tests in a separate branch, which isn't part of this PR.

[kbroman]

Thanks, @aaronwolen! I've incorporated your code into the devel branch. I also added a test and added a small bit to the documentation for read.cross and write.cross.