Description Usage Arguments Value Author(s) Examples
This function is to generate DEqMS outputs in a data frame.
1 | outputResult(fit, coef_col=1)
|
fit |
an list object produced by spectraCounteBayes function |
coef_col |
is an integer indicating the column of fit$coefficients for which corresponding t-statistics and p-values are extracted in the output |
a data frame object with the last three columns being: sca.t - Peptide or Spectra Count Adjusted posterior t-value sca.P.Value - Adjusted posterior p-value sca.adj - sca.P.Value adjusted by BH method
Yafeng Zhu
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | library(ExperimentHub)
eh = ExperimentHub(localHub=TRUE)
query(eh, "DEqMS")
dat.psm = eh[["EH1663"]]
dat.psm.log = dat.psm
dat.psm.log[,3:12] = log2(dat.psm[,3:12])
dat.gene.nm = medianSweeping(dat.psm.log,group_col = 2)
psm.count.table = as.data.frame(table(dat.psm$gene)) # generate PSM count table
rownames(psm.count.table)=psm.count.table$Var1
cond = c("ctrl","miR191","miR372","miR519","ctrl",
"miR372","miR519","ctrl","miR191","miR372")
sampleTable <- data.frame(
row.names = colnames(dat.psm)[3:12],
cond = as.factor(cond)
)
gene.matrix = as.matrix(dat.gene.nm)
design = model.matrix(~cond,sampleTable)
fit1 <- eBayes(lmFit(gene.matrix,design))
# add PSM count for each gene
fit1$count <- psm.count.table[rownames(fit1$coefficients),2]
fit2 = spectraCounteBayes(fit1)
DEqMS.results = outputResult(fit2, coef_col=3)
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