modules/anota2seq_anota2seqrun
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
Description
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
Input
The column in the sample sheet that should be used to define groups for
comparison
The value within the contrast_variable column of the sample sheet that
should be used to derive the reference samples
The value within the contrast_variable column of the sample sheet that
should be used to derive the target samples
Output
anota2seq results for the ‘translated mRNA’ analysis, describing differences in RNA levels across conditions for Ribo-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.
.translated_mRNA.anota2seq.results.tsv anota2seq results for the ‘translated mRNA’ analysis, describing differences in RNA levels across conditions for RNA-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.
.total_mRNA.anota2seq.results.tsv anota2seq results for the ‘translated mRNA’ analysis, describing differences in translation across conditions, being differences in translated RNA levels not explained by total RNA levels. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.
.translation.anota2seq.results.tsv anota2seq results for the ‘translated mRNA’ analysis, describing buffering across conditions, being stable levels of translated RNA (from riboseq samples) across conditions, despite changes in total mRNA. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.
.buffering.anota2seq.results.tsv anota2seq results for the ‘mRNA abunance’ analysis, describing changes across conditions consistent between total mRNA and translated RNA (RNA-seq and Riboseq samples). See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.
.mRNA_abundance.anota2seq.results.tsv A fold change plot in PNG format, from anota2seq’s anota2seqPlotFC()
method.
.fold_change.png The distribution of p-values and adjusted p-values for the omnibus
interaction (both using densities and histograms). The second page of
the pdf displays the same plots but for the RVM statistics if RVM is
used.
.interaction_p_distribution.pdf Summary plot for assessing normal distribution of regression residuals.
.residual_distribution_summary.jpeg QC plot showing residuals against fitted values.
.residual_vs_fitted.jpeg QC plot showing the CDF of variance (theoretical vs empirical), all
contrasts.
.rvm_fit_for_all_contrasts_group.jpg QC plot showing the CDF of variance (theoretical vs empirical), for
interactions.
.rvm_fit_for_interactions.jpg QC plot showing the CDF of variance (theoretical vs empirical), for
omnibus group.
.rvm_fit_for_omnibus_group.jpg Bar graphs of the frequencies of outlier dfbetas using different
dfbetas thresholds.
.simulated_vs_obt_dfbetas_without_interaction.pdf 