gradox {JMDplots}

R Documentation

Carbon oxidation state of proteins inferred from metagenomes in redox gradients

Description

Plots from the paper by Dick et al. (2019).

Usage

  gradox1(pdf = FALSE)
  gradox2(pdf = FALSE)
  gradoxS1(pdf = FALSE)
  gradoxS2(pdf = FALSE)
  gradox3(mout, pout, pdf = FALSE)
  gradox4(mout, pout, pdf = FALSE)
  gradox5(pdf = FALSE, maxdepth = 500)

Arguments

pdf	logical, make a PDF file?
mout	list, value returned by gradoxS1 (DNA ZC)
pout	list, value returned by gradoxS2 (protein ZC)
maxdepth	numeric, maximum sample depth (meters)

Details

This table gives a brief description of each function.

gradox1	Some general characteristics of ZC of DNA, RNA, and proteins
gradox2	Selected plots of metagenomic DNA, RNA, and protein ZC
gradoxS1	All plots of DNA and RNA ZC
gradoxS2	All plots of protein ZC
gradox3	ZC of proteins vs DNA (metagenomes and metatranscriptomes)
gradox4	Thermodynamic calculations of relative stabilities along redox gradients
gradox5	ZC of reads classified to selected abundant species

Files in extdata/gradox

The files were generated by processing source FASTA files using the “ARAST” workflow; see the paper (Dick et al., 2019) and the Zenodo record (doi:10.5281/zenodo.2314933) for more information. The R object in each RDS file is a list with both metagenomic and metatranscriptomic data and names of list elements corresponding to original CSV files. Files whose names contain ‘⁠MGD⁠’, ‘⁠MGR⁠’, or ‘⁠MGP⁠’ are derived from metegenomic datasets; those with ‘⁠MTD⁠’, ‘⁠MTR⁠’, or ‘⁠MTP⁠’ are derived from metatranscriptomic datasets.

Tables_S1-S2.xlsx

Accession numbers used and sequence processing statistics.

MGD.rds

DNA nucleobase compositions for groups of sequences sampled from source FASTA files that have been trimmed, normalized, and dereplicated. For metatranscriptomes, sequences classified as rRNA by FragGeneScan (Rho et al., 2010) were removed.

MGR.rds

RNA nucleobase compositions for groups of sequences sampled from coding DNA FASTA files generated by FragGeneScan.

MGP.rds

Protein amino acid compositions for groups of sequences sampled from protein FASTA files generated by FragGeneScan.

mkrds.R

Script to make the RDS files from multiple CSV files produced by the “ARAST” workflow.

one_percent

Files generated by using Kraken (Wood and Salzberg, 2014) report files to calculate taxon abundances as a percentage of the number of classified reads, then extracting species that make up at least 1 percent of the classified reads.

AA_codon.csv

Codon usage data for Prochlorococcus marinus str. AS9601 and Thermus thermophilus HB8 (taxids 146891 and 300852), obtained from the Codon Usage Database (Nakamura et al., 2000).

References

Dick JM, Yu M, Tan J and Lu A (2019) Changes in carbon oxidation state of metagenomes along geochemical redox gradients. Front. Microbiol. 10, 120. doi:10.3389/fmicb.2019.00120

Nakamura Y, Gojobori T and Ikemura T (2000) Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 28, 292. doi:10.1093/nar/28.1.292

Rho M, Tang H and Ye Y (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res. 38, e191. doi:10.1093/nar/gkq747

Wood DE and Salzberg SL (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, R46. doi:10.1186/gb-2014-15-3-r46

Examples

gradox1()

mout <- gradoxS1()
pout <- gradoxS2()
gradox3(mout, pout)

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