RnaModificationResults: RNA modification detection result output from xPore.

In daewon-gong/NanoPlotR: Nanopore Sequencing Based RNA Modification Detection Visualization

Description

RNA modification detection result output from xPore.

Usage

RnaModificationResults

Format

Dataframe with 129 rows and 18 variables

id

Transcript or gene id

position

Transcript or gene position

kmer

5-mer where modified base sits in the middle if modified.

diff_mod_rate_KO_vs_WT

Differential modification rate between condition1 and condition2 (modification rate of condition1 - modification rate of condition2).

z_score_KO_vs_WT

Z score obtained from z-test of the differential modification rate.

pval_KO_vs_WT

Significance level from z-test of the differential modification rate.

mod_rate_KO.rep1

Modification rate of a replicate 1 of KO condition.

mod_rate_WT.rep1

Modification rate of a replicate 1 of KO condition.

coverage_KO.rep1

Read coverage of genes in replicate 1 of KO condition.

coverage_WT.rep1

Read coverage of genes in replicate 1 of WT condition.

mu_unmod

Inferred mean of the unmodified RNAs distribution.

mu_mod

Inferred mean of the modified RNAs distribution.

sigma2_unmod

Inferred sigma^2 of the unmodified RNAs distribution.

sigma2_mod

Inferred sigma^2 of the modified RNAs distribution.

conf_mu_unmod

Confidence level of mu_unmod compared to the unmodified reference signal.

conf_mu_mod

Confidence level of mu_unmod compared to the unmodified reference signal.

mod_assignment

Lower if mu_mod < mu_unmod and higher if mu_mod > mu_unmod

t.test

P value of one-tailed t-test

Source

(Pratanwanich et al., 2021)

References

Pratanwanich, P. N., Yao, F., Chen, Y., Koh, C. W. Q., Wan, Y. K., Hendra, C., Poon, P., Goh, Y. T., Yap, P. M. L., Chooi, J. Y., Chng, W. J., Ng, S. B., Thiery, A., Goh, W. S. S., & Göke, J. (2021). Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. Nature Biotechnology,39(11), 1394–1402. https://doi.org/10.1038/s41587-021-00949-w

Examples

## Not run: 
 RnaModificationResults

## End(Not run)

daewon-gong/NanoPlotR documentation built on Dec. 19, 2021, 8:02 p.m.