| aoscp {JMDplots} | R Documentation |
Plots from the paper by Dick (2014).
aoscp1(pdf = FALSE)
aoscp2(pdf = FALSE)
aoscp3(png = FALSE, pdf = FALSE, outline = FALSE)
aoscp4(pdf = FALSE)
aoscp5(pdf = FALSE, file = NULL)
aoscp6(pdf = FALSE)
pdf |
logical, make a PDF file? |
png |
logical, make the base PNG file (no labels)? |
outline |
logical, draw only the outlines? |
file |
character, file with amino acid compositions of organisms |
This table gives a brief description of each function.
aoscp1 | ZC of amino acids vs ZC of RNA codons and hydropathy index of amino acids |
aoscp2 | Histograms of ZC of all human proteins and human membrane proteins |
aoscp3 | Drawing of yeast cell color-coded with median ZC of proteins in different locations |
aoscp4 | ZC and Eh ranges in yeast and ER-cytoplasm electron-transfer scheme |
aoscp5 | Average oxidation state of carbon in proteins from different organisms |
aoscp6 | ZC and Topt of different rubiscos and thermodynamic comparison |
NOTE: for the default file = NULL in aoscp5, values of ZC are taken from the packaged file Zc_refseq.csv.xz (see below).
If file is not NULL, then value of ZC are calculated from the amino acid compositions and the file Zc_refseq.csv is written to the working directory.
SGD_associations.csv.xzFor yeast genes, this table lists the accessions, SGDID, and the association to cellular components in the Gene Ontology, derived from gene_association.sgd.gz, protein_properties.tab and go_terms.tab downloaded from https://www.yeastgenome.org/ on 2013-08-24. All gene associations with the NOT qualifier were removed, as were those without a matching entry in protein_properties.tab (e.g. RNA-coding genes).
Zc_HUMAN.csv.xz, Zc_membrane.csv.xzCompilations of the values of ZC for human proteins and human membrane proteins.
Values in Zc_HUMAN.csv were calculated from protein sequences in HUMAN.fasta.gz, downloaded from https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/ on 2013-08-24 (file dated 2013-07-24).
Values in Zc_membrane.csv were calculated from protein sequences in all *.fa files in Additional File 2 of Almén et al. (2009).
NOTE: To save space in the package, the accession and length columns have been removed from these files; the complete files are present in the Supplementary data of Dick (2014).
codons.csvIn the first column, the three-letter abbreviations for each of the RNA codons; in the second column, the names of the corresponding amino acids.
rubisco.csvUniProt IDs for Rubisco and optimal growth temperatures of organisms.
rubisco/*.fastaFASTA sequence files for each Rubisco identified in table 3.
cell/*.pngPNG images for each of the cellular components used in aoscp3.
Zc_refseq.csv.xzThis file has the taxid, organism name, number of amino acids, and calculated ZC in 6758 microbial organisms.
This file was created using aoscp5(file = "protein_refseq.csv"), where "protein_refseq.csv" has the average amino acid compositions of proteins in different organisms.
That file, which is based on RefSeq release 61, is in the Supplementary data of Dick (2014) (https://royalsocietypublishing.org/doi/suppl/10.1098/rsif.2013.1095); a trimmed version of the file was previously present in CHNOSZ (to version 1.3.3).
In that file, the columns are protein (“refseq”), organism (taxonomic id), ref (names of RefSeq source files (followed by number of sequences and number of amino acids) [organism name in square brackets]), abbrv (total number of amino acids), chains (1).
The remaining columns have the average frequency of each amino acid in the proteins.
prep.RCode use to prepare the data files from various sources.
Dick JM (2014) Average oxidation state of carbon in proteins. J. R. Soc. Interface 11, 20131095. doi:10.1098/rsif.2013.1095
Almén MS, Nordström KJV, Fredriksson R and Schiöth HB (2009) Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin. BMC Biol. 7, 50. doi:10.1186/1741-7007-7-50
aoscp1()