DRomics (version 2.1-3)

Zhou: Dose-response liver and kidney transcriptomic effect of Trichloroethylene end Tetrachloroethylene in mouse

Description

RNAseq data sets for the effect of Trichloroethylene (TCE) and Tetrachloroethylene (PCE) on mouse liver and kidney. Each of those environmental contaminants was administered by gavage in aqueous vehicle to male B6C3F1/J mice, within a dose-reponse design including five doses plus the control.

Usage

data(Zhou_kidney_pce)
data(Zhou_kidney_tce)
data(Zhou_liver_pce)
data(Zhou_liver_tce)

Format

Zhou_kidney_pce, Zhou_kidney_tce, Zhou_liver_pce nd Zhou_liver_tce each contains one row per transcript, with the first column corresponding to the identifier of each transcript, and the other columns giving the count of reads for each replicate at each dose. In the first line, after the name for the identifier column, we have the tested doses for each corresponding replicate.

Examples

# NOT RUN {
# (1) load of data
#
data(Zhou_kidney_pce)
head(Zhou_kidney_pce)
str(Zhou_kidney_pce)

data(Zhou_kidney_tce)
head(Zhou_kidney_tce)

data(Zhou_liver_pce)
head(Zhou_liver_pce)

data(Zhou_liver_tce)
head(Zhou_liver_tce)

# }
# NOT RUN {
# (2) import, check, normalization and transformation of a sample
# of one of those datasets
#
d <- Zhou_kidney_pce[1:501, ]
(o <- RNAseqdata(d))
plot(o)


# (3) analysis of the whole dataset (for kidney and PCE)
# (may be long to run)

d <- Zhou_kidney_pce
(o <- RNAseqdata(d))
plot(o)
(s <- itemselect(o, select.method = "quadratic", FDR = 0.01))
(f <- drcfit(s, progressbar = TRUE))
head(f$fitres)

plot(f) 
plot(f, dose_log_trans = TRUE)
plot(f, plot.type = "dose_residuals")

r <- bmdcalc(f, z = 1)
plot(r) 
if (require(ggplot2))
  plot(r) + scale_x_log10() # same plot in log scale of BMD
plot(r, by = "trend")
head(r$res)

# }
# NOT RUN {
# }