R: Contact Map Consensus Filtering

filter.cmap {bio3d} | R Documentation

## Contact Map Consensus Filtering

### Description

This function filters a tridimensional contact matrix (NxNxZ), where N is the residue number and Z is the simulation number) selecting only contacts present in at least P simulations.

### Usage

    filter.cmap(cm, cutoff.sims = NULL)

### Arguments

`cm` | An array of dimensions NxNxZ or a list of NxN matrices containing binary contact values as obtained from `cmap`. Here, ‘N’ is the residue number and ‘Z’ the simulation number. The matrix elements should be 1 if two residues are in contact and 0 if they are not in contact.
`cutoff.sims` | A single element numeric vector corresponding to the minimum number of simulations a contact between two residues must be present. If not, it will be set to 0 in the output matrix.

### Value

The output matrix is a nXn binary matrix (n = residue number). Elements equal to 1 correspond to residues in contact, elements equal to 0 to residues not in contact.

### See Also

`cmap`, `plot.cmap`

### Examples

    ## Not run:
       ## load example data
      pdbfile <- system.file("examples/hivp.pdb", package="bio3d")
      pdb <- read.pdb(pdbfile)

      trtfile <- system.file("examples/hivp.dcd", package="bio3d")
      trj <- read.dcd(trtfile, verbose=FALSE)

      ## split the trj example in two
      num.of.frames <- dim(trj)[1]
      trj1 <- trj[1:(num.of.frames/2),]
      trj2 <- trj[((num.of.frames/2)+1):num.of.frames,]

      ## Lets work with Calpha atoms only
      ca.inds <- atom.select(pdb, "calpha")
      #noh.inds <- atom.select(pdb, "noh")

      ## calculate single contact map matrices
      cms <- list()
      cms[[1]] <- cmap(trj1[,ca.inds$xyz], pcut=0.3, scut=0, dcut=7, mask.lower=FALSE)
      cms[[2]] <- cmap(trj1[,ca.inds$xyz], pcut=0.3, scut=0, dcut=7, mask.lower=FALSE)

      ## calculate average contact matrix
      cm.filter <- filter.cmap(cms, cutoff.sims=2)

      ## plot the result
      par(pty="s", mfcol=c(1,3))
      plot.cmap(cms[[1]])
      plot.cmap(cms[[2]])
      plot.cmap(cm.filter)

    ## End(Not run)

[Package bio3d version 2.3-4 Index]