The RF JackKnife takes one or more XML reactivity files, and a set of reference RNA structures in dotbracket notation, and iteratively calls rf-fold by tuning the slope and intercept folding parameters. This is useful to calibrate the folding parameters for a specific probing reagent or experiment type.
It produces 3 CSV tables respectively containing the positive predictive value (PPV), sensitivity, and the geometric mean of the 2 values for each slope/intercept pair.
R can be used to easily generate heatmaps using these CSV tables:
library(gplots)
library(RColorBrewer)
csv<-read.csv("geometric_mean.csv", sep = ";", check.names = FALSE)
row.names(csv)<-csv$Mean
csv<-csv[,-1]
csv<-data.matrix(csv)
heatmap.2(csv[nrow(csv):1,], col = rev(brewer.pal(11, "Spectral")), trace = "none", cellnote = round(csv[nrow(csv):1,], digits = 2), notecol = "black", Rowv = FALSE, Colv = FALSE, dendrogram = "none", xlab = "Intercept (kcal/mol)", ylab = "Slope (kcal/mol)", key = FALSE)
Usage
To list the required parameters, simply type:
$ rf-jackknife -h
| Parameter | Type | Description |
|---|---|---|
| -r or --reference | string | A file containing reference structures in Vienna format (dotbracket notation) |
| -p or --processors | int | Number of processors to use (Default: 1) |
| -o or --output-dir | string | Output directory (Default: rf_jackknife/) |
| -t or --tmp-dir | string | Temporary directory (Default: ) |
| -ow or --overwrite | Overwrites output directory (if the specified path already exists) | |
| -sl or --slope | float,float | Range of slope values to test (Default: 0,5) |
| -in or --intercept | float,float | Range of intercept values to test (Default: -3,0) |
| -ss or --slope-step | float | Step for testing slope values (Default: 0.2) |
| -is or --intercept-step | float | Step for testing intercept values (Default: 0.2) |
| -x or --relaxed | Uses relaxed criteria (described in Deigan et al., 2009) to calculate PPV and sensitivity | |
| -kn or --keep-noncanonical | Keeps non-canonical basepairs in reference structure | |
| -kp or --keep-pseudoknots | Keeps pseudoknotted basepairs in reference structure | |
| -kl or --keep-lonelypairs | Keeps lonely basepairs (helices of length 1 bp) in reference structure | |
| -i or --ignore-sequence | Ignores sequence differences (e.g. SNVs) between the compared structures | |
| -m or --median | Reports the median PPV/sensitivity value between all reference structures Note: by default, the geometric mean of PPV/sensitivity values is reported |
|
| -am or --arithmetic-mean | Reports the arithmetic mean of PPV/sensitivity values between all reference structures Note: by default, the geometric mean of PPV/sensitivity values is reported |
|
| -rf or --rf-fold | string | Path to rf-fold executable (Default: assumes rf-fold is in PATH) |
| -rp or --rf-fold-params | string | Manually specify additional RF Fold parameters (e.g. -rp "-md 500 -m 2") |
Output CSV files
RF PeakCall produces 3 CSV files, one for PPV, one for sensitivity, and one with the geometric mean of the 2 values, with intercept values on the x-axis, and slope values on the y-axis