In going through the user guide vignette for derfinder and looking up function docs for more details, I came across the suggestion that the chromosome naming style and the species should be specified, either as arguments to certain commands, or globally for the session. It feels like such parameters would have a set of pre-determined valid values, rather than just free-text.
However I cannot find any more documentation on these anywhere on the web or the vignettes, such as what the actual values are for chromosome style or what the rules are for the species values. The function documentation in derfinder is quite minimalistic, as if many things are expected prior knowledge or blatantly obvious.

Any pointers to put me in the right direction would be much appreciated!

Hi,

The documentation you are looking for is in the extendedMapSeqlevels() function. There you'll see that it refers to names(GenomeInfoDb::genomeStyles()) for the species names.

> names(GenomeInfoDb::genomeStyles())
 [1] "Arabidopsis_thaliana"     "Caenorhabditis_elegans"   "Canis_familiaris"        
 [4] "Cyanidioschyzon_merolae"  "Drosophila_melanogaster"  "genomeMappingTbl.csv"    
 [7] "Homo_sapiens"             "Mus_musculus"             "Oryza_sativa"            
[10] "Populus_trichocarpa"      "Rattus_norvegicus"        "Saccharomyces_cerevisiae"
[13] "Zea_mays"

From there you can then find the style names:

> head(GenomeInfoDb::genomeStyles()$Homo_sapiens)
  circular auto   sex NCBI UCSC dbSNP Ensembl
1    FALSE TRUE FALSE    1 chr1   ch1       1
2    FALSE TRUE FALSE    2 chr2   ch2       2
3    FALSE TRUE FALSE    3 chr3   ch3       3
4    FALSE TRUE FALSE    4 chr4   ch4       4
5    FALSE TRUE FALSE    5 chr5   ch5       5
6    FALSE TRUE FALSE    6 chr6   ch6       6

extendedMapSeqlevels()'s documentation includes links to functions from the GenomeInfoDb package that describe more details.

Best, Leonardo

Session info details:

> packageVersion('derfinder')
[1] ‘1.11.5’
> packageVersion('GenomeInfoDb')
[1] ‘1.13.4’