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write.csv.R

write.csv.Rd

Save summaries of partitioned breeding values to CSV files on disk for further analyses of processing with other software or just for saving (backing up) results.

Usage

write.csv(...)

# S3 method for default
write.csv(...)

# S3 method for AlphaPart
write.csv(x, file, traitsAsDir = FALSE, csv2 = TRUE, row.names = FALSE, ...)

# S3 method for summaryAlphaPart
write.csv(x, file, traitsAsDir = FALSE, csv2 = TRUE, row.names = FALSE, ...)

Arguments

...

Other options passed to write.csv2 or write.csv.

x

AlphaPart, object returned from AlphaPart function or summaryAlphaPart, object returned from summary.AlphaPart function.

file

Character, file name with or without .csv extension, e.g., both "file" and "file.csv" are valid.

traitsAsDir

Logical, should results be saved within trait folders; the construction is file.path(dirname(file), trait, basename(file)); folders are created if they do not exist.

csv2

Logical, export using write.csv2 or write.csv.

row.names

Logical, export row names as well?

Value

It contains:

  • write.csv - see write.csv for details.

  • write.csv.AlphaPart - for each trait (list component in x) a file is saved on disk with name "AlphaPart_trait.csv", where the file will hold original data and breeding value partitions. With traitsAsDir=TRUE files are saved as "trait/file_trait.csv". File names are printed on screen during the process of export and at the end invisibly returned.

  • write.csv.summaryAlphaPart - for each trait (list component in x) a file partitions named "file_trait.csv" is saved on disk. With traitsAsDir=TRUE files are saved as "trait/file_trait_*.csv". File names are printed on screen during the process of export and at the end invisibly returned.

Details

Function write.csv from the utils package works when exported object is a data.frame or a matrix. This is an attempt to make this function generic so that one can define write.csv methods for other objects.

Methods (by class)

  • default: Default write.csv method.

  • AlphaPart: Save partitioned breeding values to CSV files on disk on disk for further analyses or processing with other software or just for saving (backing up) results.

  • summaryAlphaPart: Save summaries of partitioned breeding values to CSV files on disk for further analyses of processing with other software or just for saving (backing up) results.

See also

write.csv help page on the default write.csv and write.csv2 methods in the utils package; summary.AlphaPart and AlphaPart help pages on the objects of summaryAlphaPart and AlphaPart classes.

Examples

## Partition additive genetic values
res <- AlphaPart(x=AlphaPart.ped, colPath="country", colBV=c("bv1", "bv2"))
#> 
#> Size:
#>  - individuals: 8 
#>  - traits: 2 (bv1, bv2)
#>  - paths: 2 (domestic, import)
#>  - unknown (missing) values:
#> bv1 bv2 
#>   0   0 

## Write summary on the disk and collect saved file names
fileName <- file.path(tempdir(), "AlphaPart")
ret <- write.csv(x=res, file=fileName)
#> /tmp/RtmpGflKKv/AlphaPart_bv1.csv 
#> /tmp/RtmpGflKKv/AlphaPart_bv2.csv 
print(ret)
#> [1] "/tmp/RtmpGflKKv/AlphaPart_bv1.csv" "/tmp/RtmpGflKKv/AlphaPart_bv2.csv"
file.show(ret[1])

## Clean up
files <- dir(path=tempdir(), pattern="AlphaPart*")
unlink(x=files)