fpSim {ChemmineR} | R Documentation

## Fingerprint Search

### Description

Search function for fingerprints, such as PubChem or atom pair fingerprints. Enables structure similarity comparisons, searching and clustering.

### Usage

    fpSim(x, y, sorted=TRUE, method="Tanimoto",
    		addone=1, cutoff=0, top="all", alpha=1, beta=1,
    		parameters=NULL,scoreType="similarity")

### Arguments

`x` | Query molecule of class `numeric`, `FP` or `FPset` (of length one) containing binary fingerprint data. Both `x` and `y` need to have the same number of bits and should contain the same type of fingerprints.
`y` | Subject molecule(s) of class `numeric`, `matrix`, `FP` or `FPset` containing binary fingerprint data.
`sorted` | return results sorted or unsorted
`method` | Similarity coefficient to return. One can choose here from several predefined similarity measures: "Tanimoto" (default), "Euclidean", "Tversky" or "Dice". Alternatively, one can pass on any custom similarity function containing the arguments a, b, c and d. For instance, one can define "myfct <- function(a, b, c, d) c/(alpha*a + beta*b + c)" and then pass on `method=myfct`. The variable 'c' is the number of "on-bits" common in both compounds, 'd' is the number of "off-bits" common in both compounds, and 'a' and 'b' are the number of "on-bits" that are unique in one or the other compound, respectively. The predefined methods will run a C++ version of this function which is about twice as fast as the R version. When a custom similarity function is given however, it will fall back to using the R version.
`addone` | Value to add to numerator and denominator of similarity coefficient to avoid devision by zero when fingerprint(s) contain only "off-bits" (zeros). Note: if `addone > 0` then fingerprints with no "on-bits" will receive the highest similarity score. Typically, this occurs only with extremely small molecules.
`cutoff` | allows to restrict results to hits above a similarity cutoff value; default `cutoff=0` returns results for all compounds in `y`.
`top` | allows to restrict number of subject molecules to return; default `top="all"` returns results for all compounds in `y` above `cutoff` value.
`alpha` | Only used when method="Tversky". Allows to specify the weighting variable 'alpha' of the Tversky index: c/(alpha*a + beta*b + c)
`beta` | Only used when method="Tversky". Allows to specify the weighting variable 'beta' of the Tversky index.
`parameters` | Parameters for computing Z-scores, E-values, and p-values. Pass this data if you want these scores returned. This data can be generated with the `genParameters` function.
`scoreType` | If using the `parameters` argument, this argument specified which type of score the `cutoff` and `sorted` arguments should be applied to. It should be one of "similarity" (default), "zscore", "evalue", or "pvalue".

### Value

Returns `numeric vector` with similarity coefficients as values and compound identifiers as names.

### Author(s)

Thomas Girke, Kevin Horan

### References

Tanimoto similarity coefficient: Tanimoto TT (1957) IBM Internal Report 17th Nov see also Jaccard P (1901) Bulletin del la Societe Vaudoisedes Sciences Naturelles 37, 241-272.

PubChem fingerprint specification: ftp://ftp.ncbi.nih.gov/pubchem/specifications/pubchem_fingerprints.txt

### See Also

Functions: `fp2bit`

### Examples

    ## Load PubChem SDFset sample
    data(sdfsample); sdfset <- sdfsample
    cid(sdfset) <- sdfid(sdfset)

    ## Convert base 64 encoded fingerprints to character vector or binary matrix
    fpset <- fp2bit(sdfset)

    ## Alternatively, one can use atom pair fingerprints
    ## Not run:
    fpset <- desc2fp(sdf2ap(sdfset))

    ## End(Not run)

    ## Pairwise compound structure comparisons
    fpSim(x=fpset[1], y=fpset[2], method="Tanimoto")

    ## Structure similarity searching: x is query and y is fingerprint database
    fpSim(x=fpset[1], y=fpset)

    ## Controlling the output
    fpSim(x=fpset[1], y=fpset, method="Tversky", cutoff=0.4, top=4, alpha=0.5, beta=1)

    ## Use custom distance function
    myfct <- function(a, b, c, d) c/(a+b+c+d)
    fpSim(x=fpset[1], y=fpset, method=myfct)

    ## Compute fingerprint-based Tanimoto similarity matrix
    simMA <- sapply(cid(fpset), function(x) fpSim(x=fpset[x], fpset, sorted=FALSE))

    ## Hierarchical clustering with simMA as input
    hc <- hclust(as.dist(1-simMA), method="single")

    ## Plot hierarchical clustering tree
    plot(as.dendrogram(hc), edgePar=list(col=4, lwd=2), horiz=TRUE)

[Package ChemmineR version 3.40.0 Index]