plotDStructurome {dStruct}

R Documentation

Plots differentially reactive regions.

Description

Given the table of results from dStruct or dStructGuided and the corresponding lists with reactivity scores for all transcripts, this function saves a PDF file with detailed visualizations of reactivities for all differential regions.

Usage

plotDStructurome(
  rl,
  diff_regions,
  outfile,
  fdr = 0.05,
  ylim = c(-0.05, 3),
  del_d_cutoff = 0.01
)

Arguments

rl	List of dataframes of reactivities for each sample.
diff_regions	Output from dStruct or dStructGuided containing coordinates of regions with significance of differentially reactivity.
outfile	The name for pdf file which will be saved.
fdr	FDR threshold for plotted regions.
ylim	Y-axis limits for plots.
del_d_cutoff	Minimum effect size for plotted regions specified in terms of median difference of the between-group and within-group d-scores.

Value

Saves a PDF for all differentially reactive regions. Returns NULL.

Author(s)

Krishna Choudhary

References

Choudhary, K., Lai, Y. H., Tran, E. J., & Aviran, S. (2019). dStruct: identifying differentially reactive regions from RNA structurome profiling data. Genome biology, 20(1), 1-26.

Examples

#Load data from Lai et al., 2019
data(lai2019)

#Run dStruct in de novo discovery mode for all the transcripts in this data in one step.
res <- dStructome(lai2019, 3, 2, batches= TRUE, min_length = 21,
    between_combs = data.frame(c("A3", "B1", "B2")),
    within_combs = data.frame(c("A1", "A2", "A3")),
    ind_regions = TRUE, processes = 1)

#Plot the significant results and save to a PDF file.
plotDStructurome(rl = lai2019,
    diff_regions = res,
    outfile = "significantly_differential_regions",
    fdr = 0.05,
    ylim = c(-0.05, 3))

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