Commit 6191ee1f authored by Digp's avatar Digp
Browse files

Updating package for publication. Commit 1

parent 4628b460
Pipeline #3792 skipped
......@@ -21,9 +21,9 @@ function(ntIDs) {
## "filter_pyle" reproduces the iterative process of RMSD comparison to chose
## "filter_helical" reproduces the iterative process of RMSD comparison to chose
## an helical nucleotide of reference
filter_pyle <-
filter_helical <-
function(ntinfo, helicalntID, RMSD, bandwidths=c(40,40), cutoff=0.85) {
twideMatrix <- t(acast(RMSD, nt1~nt2, value.var="rmsd"))
......@@ -21,7 +21,7 @@ cat("Getting data\n")
## ----------------------------------------------------------------------------
## Get latest Leontist non-redundant list of RNA structures
infochains <- getLeontisList(threshold="2.5A", as.df=TRUE)
infochains <- getRNAList(threshold="2.5A", as.df=TRUE)
## Get structural data
ntinfo <- pipeNucData(pdbID=infochains$pdb, model=infochains$model,
......@@ -56,7 +56,7 @@ RMSD_calc <- apply(FUN=pwrmsd, MARGIN=1, X=pairwise)
RMSD <- data.frame(nt1=pairwise[, 1], nt2=pairwise[, 2], rmsd=RMSD_calc)
## Apply Pyle method
ref <- filter_pyle(ntinfo=ntinfo, helicalntID=HDR[[1]], RMSD=RMSD)
ref <- filter_helical(ntinfo=ntinfo, helicalntID=HDR[[1]], RMSD=RMSD)
pairs <- data.frame(usefulnt=usefulnt, reference=rep(ref, length(usefulnt)))
RMSD2 <- apply(FUN=pwrmsd, MARGIN=1, X=pairs)
......@@ -7,7 +7,7 @@ VeriNA3d is an R package for the analysis of Nucleic Acid structural data. The s
## Installation
Instructions for Unix systems
1- Make sure you have all the dependencies already installed in R. If not the case, open R and run:
......@@ -16,17 +16,9 @@ Instructions for Unix systems
2- Install veriNA3d according with your R version:
For R >= 3.5
install.packages("", repos = NULL)
If you have R-3.4:
install.packages("", repos = NULL)
The whole package has been developed and tested in R-3.5, which makes it the recommended option. Furthermore, using R-3.5 speeds up the cifParser function, which has a dramatic effect when working with large mmCIF files. The package has been also made available for R-3.4 since some unix users are experiencing problems when installing R-3.5.
install.packages("", repos = NULL)
3- To start using it, just load the package!
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