This object contains the theoretical GC content for each provided species, for both the genome and transcriptome, where available.
gcTheoreticalAn object of class TheoreticalGC of length 1.
The object is defined with the S4 class TheoreticalGC.
Species for which information is available can be found using
the command gcAvail(gcTheoretical) and selecting the appropriate type.
Metadata is accessible using mData(gcTheoretical).
All GC content was calculated using code from https://github.com/mikelove/fastqcTheoreticalGC using BSgenome packages. This provides a default set of GC content data for common organisms generated using 100bp reads/fragments and 1e6 reads.
gcAvail
## Check which genomes are included
gcAvail(gcTheoretical, "Genome")
#> # A tibble: 24 × 4
#> Name Group Source Version
#> <chr> <chr> <chr> <chr>
#> 1 Alyrata Plants JGI V1.0
#> 2 Amellifera Animals UCSC apiMel2
#> 3 Athaliana Plants TAIR Arapot11
#> 4 Btaurus Animals UCSC bosTau8
#> 5 Celegans Animals UCSC ce11
#> 6 Cfamiliaris Animals UCSC canFam3
#> 7 Dmelanogaster Animals UCSC dm6
#> 8 Drerio Animals UCSC danRer10
#> 9 Ecoli Bacteria NCBI 2008/08/05
#> 10 Gaculeatus Other UCSC gasAcu1
#> # ℹ 14 more rows
## Check which transcriptomes are included
gcAvail(gcTheoretical, "Transcriptome")
#> # A tibble: 13 × 4
#> Name Group Source Version
#> <chr> <chr> <chr> <chr>
#> 1 Athaliana Plants TAIR Arapot11
#> 2 Btaurus Animals UCSC bosTau8
#> 3 Celegans Animals UCSC ce11
#> 4 Cfamiliaris Animals UCSC canFam3
#> 5 Dmelanogaster Animals UCSC dm6
#> 6 Drerio Animals UCSC danRer10
#> 7 Hsapiens Animals UCSC hg38
#> 8 Mmulatta Animals UCSC rheMac8
#> 9 Mmusculus Animals UCSC mm10
#> 10 Ptroglodytes Animals UCSC panTro5
#> 11 Rnorvegicus Animals UCSC rn6
#> 12 Scerevisiae Yeast UCSC sacCer3
#> 13 Sscrofa Animals UCSC susScr3