Zhou: Dose-response kidney transcriptomic effect of...

In DRomics: Dose Response for Omics

Dose-response kidney transcriptomic effect of Tetrachloroethylene in mouse

Description

RNAseq data set for the effect of Tetrachloroethylene (PCE) on mouse kidney. This environmental contaminant 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)

Format

Zhou_kidney_pce 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.

Source

Zhou, Y. H., Cichocki, J. A., Soldatow, V. Y., Scholl, E. H., Gallins, P. J., Jima, D., ... & Rusyn, I. 2017. Comparative dose-response analysis of liver and kidney transcriptomic effects of trichloroethylene and tetrachloroethylene in B6C3F1 mouse. Toxicological sciences, 160(1), 95-110.

Examples

# (1) load of data
#
data(Zhou_kidney_pce)
head(Zhou_kidney_pce)
str(Zhou_kidney_pce)



# (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)

DRomics documentation built on Feb. 16, 2023, 6:45 p.m.