Description Usage Format Details Source References Examples
Experiments and data are obtained from Yassour et. al. (2009).
1 |
A data.frame
contains 6303 rows and 5 columns:
ORF
is for gene names in character, and
YPD0.1
, YPD0.2
, YPD15.1
, and YPD15.2
are
gene expressions in positive double corresponding to 4 controlled
Yeast experiments.
The original data are available as the URL of the section of Source next.
As the section of Examples next, data are selected from SD3.xls
and
reordered by ORF
.
For further analysis, the Examples section also provides how to
convert them to phi.Obs
values either in geometric means or individually.
https://www.pnas.org/content/early/2009/02/10/0812841106
https://www.pnas.org/highwire/filestream/598612/field_highwire_adjunct_files/3/SD3.xls
Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, Luo S, Khrebtukova I, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A. (2009) “Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing.” Proc Natl Acad Sci USA 106(9):3264-9. [PMID:19208812]
Wallace E.W.J., Airoldi E.M., and Drummond D.A. “Estimating Selection on Synonymous Codon Usage from Noisy Experimental Data” Mol Biol Evol (2013) 30(6):1438–1453.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | ## Not run:
### SD3.xls is available from the URL provided in the References.
da <- read.table("SD3.xls", header = TRUE, sep = "\t", quote = "",
stringsAsFactors = FALSE)
### Select ORF, YPD0.1, YPD0.2, YPD15.1, YPD15.2.
da <- da[, c(1, 8, 9, 10, 11)]
colnames(da) <- c("ORF", "YPD0.1", "YPD0.2", "YPD15.1", "YPD15.2")
### Drop inappropriate values (NaN, NA, Inf, -Inf, and 0).
tmp <- da[, 2:5]
id.tmp <- rowSums(is.finite(as.matrix(tmp)) & tmp != 0) >= 3
tmp <- da[id.tmp, 1:5]
yassour <- tmp[order(tmp$ORF),] # cubfits::yassour
### Get geometric mean of phi.Obs and scaling similar to Wallace (2013).
GM <- apply(yassour[, -1], 1, function(x) exp(mean(log(x[x != 0]))))
phi.Obs <- GM / sum(GM) * 15000
### Get individual of phi.Obs.
GM <- apply(yassour[, -1], 1, function(x) exp(mean(log(x[x != 0]))))
phi.Obs.all <- yassour[, -1] / sum(GM) * 15000
phi.Obs.all[phi.Obs.all == 0] <- NA
## End(Not run)
|
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