Nothing
R/801-getCPI.R
In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions
Defines functions
nner
getCPICombine
getCPITensor
getPPICombine
getPPITensor
getPPIEntry
getDDICombine
getDDITensor
getDDIEntry
getDPIinner
getDPICombine
getDPITensor
getCCICombine
getCCITensor
getCCIEntry
getCDIinner
getCDICombine
getCDITensor
getCPI
getPPI
getDDI
getDPI
getCCI
getCDI
Documented in
getCCI
getCDI
getCPI
getDDI
getDPI
getPPI
.inner = function (a, b, f, ...) {
# For computing column-by-column (pseudo)-tensor product type interactions
f = match.fun(f)
apply(b, 2, function (x) apply(a, 1, function (y) f(x, y, ...)))
}
.getCPICombine = function (drugmat, protmat) {
return(cbind(drugmat, protmat))
}
.getCPITensor = function (drugmat, protmat, row, dcol, pcol) {
return(array(.inner(t(drugmat), protmat, '*'), c(row, dcol * pcol)))
}
.getPPICombine = function (protmat1, protmat2) {
return(cbind(protmat1, protmat2))
}
.getPPITensor = function (protmat1, protmat2, row, col) {
return(array(.inner(t(protmat1), protmat2, '*'), c(row, col^2)))
}
.getPPIEntry = function (protmat1, protmat2) {
return(cbind((protmat1 * protmat2), (protmat1 + protmat2)))
}
.getDDICombine = function (DNAmat1, DNAmat2) {
return(cbind(DNAmat1, DNAmat2))
}
.getDDITensor = function (DNAmat1, DNAmat2, row, col) {
return(array(.inner(t(DNAmat1), DNAmat2, '*'), c(row, col^2)))
}
.getDDIEntry = function (DNAmat1, DNAmat2) {
return(cbind((DNAmat1 * DNAmat2), (DNAmat1 + DNAmat2)))
}
.getDPIinner = function (a, b, f, ...) {
# For computing column-by-column (pseudo)-tensor product type interactions
f = match.fun(f)
apply(b, 2, function (x) apply(a, 1, function (y) f(x, y, ...)))
}
.getDPICombine = function (DNAmat, protmat) {
return(cbind(DNAmat, protmat))
}
.getDPITensor = function (DNAmat, protmat, row, dcol, pcol) {
return(array(.getDPIinner(t(DNAmat), protmat, '*'), c(row, dcol * pcol)))
}
.getCCICombine = function (drugmat1, drugmat2) {
return(cbind(drugmat1, drugmat2))
}
.getCCITensor = function (drugmat1, drugmat2, row, col) {
return(array(.inner(t(drugmat1), drugmat2, '*'), c(row, col^2)))
}
.getCCIEntry = function (drugmat1, drugmat2) {
return(cbind((drugmat1 * drugmat2), (drugmat1 + drugmat2)))
}
.getCDIinner = function (a, b, f, ...) {
# For computing column-by-column (pseudo)-tensor product type interactions
f = match.fun(f)
apply(b, 2, function (x) apply(a, 1, function (y) f(x, y, ...)))
}
.getCDICombine = function (drugmat, DNAmat) {
return(cbind(drugmat, DNAmat))
}
.getCDITensor = function (drugmat, DNAmat, row, dcol, pcol) {
return(array(.getCDIinner(t(drugmat), DNAmat, '*'), c(row, dcol * pcol)))
}
#' @title Generating Interaction Descriptors
#'
#' @description Generating Interaction Descriptors
#'
#' @details This function calculates the interaction descriptors
#' by three types of interaction:
#' \itemize{
#' \item \code{combine} - combine the two descriptor matrix,
#' result has \code{(p1 + p2)} columns
#' \item \code{tensorprod} - calculate column-by-column
#' (pseudo)-tensor product type interactions, result has
#' \code{(p1 * p2)} columns
#' \item \code{entrywise} - calculate entrywise product and
#' entrywise sum of the two matrices, then combine them,
#' result has \code{(p + p)} columns
#' }
#'
#' @param drugmat The compound descriptor matrix.
#' @param protmat The protein descriptor matrix.
#' @param type The interaction type, one or more of
#' \code{"combine"}, \code{"tensorprod"}, and \code{"entrywise"}.
#'
#' @return A matrix containing the interaction descriptors
#'
#' @keywords getCPI getCDI getDPI getPPI getDDI getCCI interaction
#'
#' @aliases getCPI
#'
#' @author Min-feng Zhu <\email{wind2zhu@@163.com}>,
#' Nan Xiao <\url{http://r2s.name}>
#'
#' @export getCPI
#'
#' @examples
#' x = matrix(1:10, ncol = 2)
#' y = matrix(1:15, ncol = 3)
#' # getCPI
#' getCPI(x, y, 'combine')
#' # getCDI
#' getCDI(x, y, 'tensorprod')
#' # getDPI
#' getDPI(x, y, type = c('combine', 'tensorprod'))
#' getDPI(x, y, type = c('tensorprod', 'combine'))
#'
getCPI = function (drugmat, protmat, type = c('combine', 'tensorprod')) {
if (!is.matrix(drugmat)) drugmat = as.matrix(drugmat)
if (!is.matrix(protmat)) protmat = as.matrix(protmat)
drugrow = nrow(drugmat)
protrow = nrow(protmat)
if (drugrow != protrow) stop('Matrix row count must match')
drugcol = ncol(drugmat)
protcol = ncol(protmat)
if (missing(type)) stop('Must provide at least one interaction type')
if (all(type == 'combine')) {
result = .getCPICombine(drugmat, protmat)
} else if (all(type == 'tensorprod')) {
result = .getCPITensor(drugmat, protmat, row = drugrow,
dcol = drugcol, pcol = protcol)
} else if (length(setdiff(type, c('tensorprod', 'combine'))) == 0L) {
result = cbind(.getCPICombine(drugmat, protmat),
.getCPITensor(drugmat, protmat, row = drugrow,
dcol = drugcol, pcol = protcol))
} else {
stop('Interaction type must be in "tensorprod" and "combine" or both')
}
return(result)
}
#' @rdname getCPI
#'
#' @aliases getPPI
#'
#' @param protmat1 The first protein descriptor matrix,
#' must have the same ncol with \code{protmat2}.
#' @param protmat2 The second protein descriptor matrix,
#' must have the same ncol with \code{protmat1}.
#'
#' @export getPPI
#'
#' @examples
#' x = matrix(1:10, ncol = 2)
#' y = matrix(5:14, ncol = 2)
#'
#' # getPPI
#' getPPI(x, y, type = 'combine')
#' getPPI(x, y, type = 'tensorprod')
#' # getDDI
#' getDDI(x, y, type = 'entrywise')
#' getDDI(x, y, type = c('combine', 'tensorprod'))
#' # getCCI
#' getCCI(x, y, type = c('combine', 'entrywise'))
#' getCCI(x, y, type = c('entrywise', 'tensorprod'))
#' getCCI(x, y, type = c('combine', 'entrywise', 'tensorprod'))
getPPI = function (protmat1, protmat2, type = c('combine', 'tensorprod',
'entrywise')) {
if (!is.matrix(protmat1)) protmat1 = as.matrix(protmat1)
if (!is.matrix(protmat2)) protmat2 = as.matrix(protmat2)
protrow1 = nrow(protmat1)
protrow2 = nrow(protmat2)
if (protrow1 != protrow2) stop('Matrix row count must match')
protcol1 = ncol(protmat1)
protcol2 = ncol(protmat2)
if (protcol1 != protcol2) stop('Matrix column count must match')
if (missing(type)) stop('Must provide at least one interaction type')
if (all(type == 'combine')) {
result = .getPPICombine(protmat1, protmat2)
} else if (all(type == 'tensorprod')) {
result = .getPPITensor(protmat1, protmat2,
row = protrow1, col = protcol1)
} else if (all(type == 'entrywise')) {
result = .getPPIEntry(protmat1, protmat2)
} else if (length(setdiff(type, c('tensorprod', 'combine'))) == 0L) {
result = cbind(.getPPICombine(protmat1, protmat2),
.getPPITensor(protmat1, protmat2,
row = protrow1, col = protcol1))
} else if (length(setdiff(type, c('tensorprod', 'entrywise'))) == 0L) {
result = cbind(.getPPITensor(protmat1, protmat2,
row = protrow1,
col = protcol1),
.getPPIEntry(protmat1, protmat2))
} else if (length(setdiff(type, c('combine', 'entrywise'))) == 0L) {
result = cbind(.getPPICombine(protmat1, protmat2),
.getPPIEntry(protmat1, protmat2))
} else if (length(setdiff(type, c('tensorprod',
'combine',
'entrywise'))) == 0L) {
result = cbind(.getPPICombine(protmat1, protmat2),
.getPPITensor(protmat1, protmat2,
row = protrow1,
col = protcol1),
.getPPIEntry(protmat1, protmat2))
} else {
stop('Interaction type must be in "tensorprod", "combine" and "entrywise"')
}
return(result)
}
#' @rdname getCPI
#'
#' @aliases getDDI
#'
#' @param DNAmat1 The first DNA descriptor matrix,
#' must have the same ncol with \code{DNAmat2}.
#' @param DNAmat2 The second DNA descriptor matrix,
#' must have the same ncol with \code{DNAmat1}.
#'
#' @export getDDI
#'
getDDI = function (DNAmat1, DNAmat2, type = c('combine', 'tensorprod',
'entrywise')) {
if (!is.matrix(DNAmat1)) DNAmat1 = as.matrix(DNAmat1)
if (!is.matrix(DNAmat2)) DNAmat2 = as.matrix(DNAmat2)
DNArow1 = nrow(DNAmat1)
DNArow2 = nrow(DNAmat2)
if (DNArow1 != DNArow2) stop('Matrix row count must match')
DNAcol1 = ncol(DNAmat1)
DNAcol2 = ncol(DNAmat2)
if (DNAcol1 != DNAcol2) stop('Matrix column count must match')
if (missing(type)) stop('Must provide at least one interaction type')
if (all(type == 'combine')) {
result = .getDDICombine(DNAmat1, DNAmat2)
} else if (all(type == 'tensorprod')) {
result = .getDDITensor(DNAmat1, DNAmat2,
row = DNArow1, col = DNAcol1)
} else if (all(type == 'entrywise')) {
result = .getDDIEntry(DNAmat1, DNAmat2)
} else if (length(setdiff(type, c('tensorprod', 'combine'))) == 0L) {
result = cbind(.getDDICombine(DNAmat1, DNAmat2),
.getDDITensor(DNAmat1, DNAmat2,
row = DNArow1, col = DNAcol1))
} else if (length(setdiff(type, c('tensorprod', 'entrywise'))) == 0L) {
result = cbind(.getDDITensor(DNAmat1, DNAmat2,
row = DNArow1,
col = DNAcol1),
.getDDIEntry(DNAmat1, DNAmat2))
} else if (length(setdiff(type, c('combine', 'entrywise'))) == 0L) {
result = cbind(.getDDICombine(DNAmat1, DNAmat2),
.getDDIEntry(DNAmat1, DNAmat2))
} else if (length(setdiff(type, c('tensorprod',
'combine',
'entrywise'))) == 0L) {
result = cbind(.getDDICombine(DNAmat1, DNAmat2),
.getDDITensor(DNAmat1, DNAmat2,
row = DNArow1,
col = DNAcol1),
.getDDIEntry(DNAmat1, DNAmat2))
} else {
stop('Interaction type must be in "tensorprod", "combine" and "entrywise"')
}
return(result)
}
#' @rdname getCPI
#'
#' @aliases getDPI
#'
#' @param DNAmat The DNA descriptor matrix.
#'
#' @export getDPI
#'
getDPI = function (DNAmat, protmat, type = c('combine', 'tensorprod')) {
if (!is.matrix(DNAmat)) DNAmat = as.matrix(DNAmat)
if (!is.matrix(protmat)) protmat = as.matrix(protmat)
DNArow = nrow(DNAmat)
protrow = nrow(protmat)
if (DNArow != protrow) stop('Matrix row count must match')
DNAcol = ncol(DNAmat)
protcol = ncol(protmat)
if (missing(type)) stop('Must provide at least one interaction type')
if (all(type == 'combine')) {
result = .getDPICombine(DNAmat, protmat)
} else if (all(type == 'tensorprod')) {
result = .getDPITensor(DNAmat, protmat, row = DNArow,
dcol = DNAcol, pcol = protcol)
} else if (length(setdiff(type, c('tensorprod', 'combine'))) == 0L) {
result = cbind(.getDPICombine(DNAmat, protmat),
.getDPITensor(DNAmat, protmat, row = DNArow,
dcol = DNAcol, pcol = protcol))
} else {
stop('Interaction type must be in "tensorprod" and "combine" or both')
}
return(result)
}
#' @rdname getCPI
#'
#' @aliases getCCI
#'
#' @param drugmat1 The first compound descriptor matrix,
#' must have the same ncol with \code{drugmat2}.
#' @param drugmat2 The second compound descriptor matrix,
#' must have the same ncol with \code{drugmat1}.
#'
#' @export getCCI
#'
getCCI = function (drugmat1, drugmat2, type = c('combine', 'tensorprod',
'entrywise')) {
if (!is.matrix(drugmat1)) drugmat1 = as.matrix(drugmat1)
if (!is.matrix(drugmat2)) drugmat2 = as.matrix(drugmat2)
drugrow1 = nrow(drugmat1)
drugrow2 = nrow(drugmat2)
if (drugrow1 != drugrow2) stop('Matrix row count must match')
drugcol1 = ncol(drugmat1)
drugcol2 = ncol(drugmat2)
if (drugcol1 != drugcol2) stop('Matrix column count must match')
if (missing(type)) stop('Must provide at least one interaction type')
if (all(type == 'combine')) {
result = .getCCICombine(drugmat1, drugmat2)
} else if (all(type == 'tensorprod')) {
result = .getCCITensor(drugmat1, drugmat2,
row = drugrow1, col = drugcol1)
} else if (all(type == 'entrywise')) {
result = .getCCIEntry(drugmat1, drugmat2)
} else if (length(setdiff(type, c('tensorprod', 'combine'))) == 0L) {
result = cbind(.getCCICombine(drugmat1, drugmat2),
.getCCITensor(drugmat1, drugmat2,
row = drugrow1, col = drugcol1))
} else if (length(setdiff(type, c('tensorprod', 'entrywise'))) == 0L) {
result = cbind(.getCCITensor(drugmat1, drugmat2,
row = drugrow1,
col = drugcol1),
.getCCIEntry(drugmat1, drugmat2))
} else if (length(setdiff(type, c('combine', 'entrywise'))) == 0L) {
result = cbind(.getCCICombine(drugmat1, drugmat2),
.getCCIEntry(drugmat1, drugmat2))
} else if (length(setdiff(type, c('tensorprod',
'combine',
'entrywise'))) == 0L) {
result = cbind(.getCCICombine(drugmat1, drugmat2),
.getCCITensor(drugmat1, drugmat2,
row = drugrow1,
col = drugcol1),
.getCCIEntry(drugmat1, drugmat2))
} else {
stop('Interaction type must be in "tensorprod", "combine" and "entrywise"')
}
return(result)
}
#' @rdname getCPI
#'
#' @aliases getCDI
#'
#' @export getCDI
#'
getCDI = function (drugmat, DNAmat, type = c('combine', 'tensorprod')) {
if (!is.matrix(drugmat)) drugmat = as.matrix(drugmat)
if (!is.matrix(DNAmat)) DNAmat = as.matrix(DNAmat)
drugrow = nrow(drugmat)
DNArow = nrow(DNAmat)
if (drugrow != DNArow) stop('Matrix row count must match')
drugcol = ncol(drugmat)
DNAcol = ncol(DNAmat)
if (missing(type)) stop('Must provide at least one interaction type')
if (all(type == 'combine')) {
result = .getCDICombine(drugmat, DNAmat)
} else if (all(type == 'tensorprod')) {
result = .getCDITensor(drugmat, DNAmat, row = drugrow,
dcol = drugcol, pcol = DNAcol)
} else if (length(setdiff(type, c('tensorprod', 'combine'))) == 0L) {
result = cbind(.getCDICombine(drugmat, DNAmat),
.getCDITensor(drugmat, DNAmat, row = drugrow,
dcol = drugcol, pcol = DNAcol))
} else {
stop('Interaction type must be in "tensorprod" and "combine" or both')
}
return(result)
}
Try the BioMedR package in your browser
Any scripts or data that you put into this service are public.
BioMedR documentation built on Nov. 17, 2017, 10:08 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions nner getCPICombine getCPITensor getPPICombine getPPITensor getPPIEntry getDDICombine getDDITensor getDDIEntry getDPIinner getDPICombine getDPITensor getCCICombine getCCITensor getCCIEntry getCDIinner getCDICombine getCDITensor getCPI getPPI getDDI getDPI getCCI getCDI
Documented in getCCI getCDI getCPI getDDI getDPI getPPI
.inner = function (a, b, f, ...) {
# For computing column-by-column (pseudo)-tensor product type interactions
f = match.fun(f)
apply(b, 2, function (x) apply(a, 1, function (y) f(x, y, ...)))
}
.getCPICombine = function (drugmat, protmat) {
return(cbind(drugmat, protmat))
}
.getCPITensor = function (drugmat, protmat, row, dcol, pcol) {
return(array(.inner(t(drugmat), protmat, '*'), c(row, dcol * pcol)))
}
.getPPICombine = function (protmat1, protmat2) {
return(cbind(protmat1, protmat2))
}
.getPPITensor = function (protmat1, protmat2, row, col) {
return(array(.inner(t(protmat1), protmat2, '*'), c(row, col^2)))
}
.getPPIEntry = function (protmat1, protmat2) {
return(cbind((protmat1 * protmat2), (protmat1 + protmat2)))
}
.getDDICombine = function (DNAmat1, DNAmat2) {
return(cbind(DNAmat1, DNAmat2))
}
.getDDITensor = function (DNAmat1, DNAmat2, row, col) {
return(array(.inner(t(DNAmat1), DNAmat2, '*'), c(row, col^2)))
}
.getDDIEntry = function (DNAmat1, DNAmat2) {
return(cbind((DNAmat1 * DNAmat2), (DNAmat1 + DNAmat2)))
}
.getDPIinner = function (a, b, f, ...) {
# For computing column-by-column (pseudo)-tensor product type interactions
f = match.fun(f)
apply(b, 2, function (x) apply(a, 1, function (y) f(x, y, ...)))
}
.getDPICombine = function (DNAmat, protmat) {
return(cbind(DNAmat, protmat))
}
.getDPITensor = function (DNAmat, protmat, row, dcol, pcol) {
return(array(.getDPIinner(t(DNAmat), protmat, '*'), c(row, dcol * pcol)))
}
.getCCICombine = function (drugmat1, drugmat2) {
return(cbind(drugmat1, drugmat2))
}
.getCCITensor = function (drugmat1, drugmat2, row, col) {
return(array(.inner(t(drugmat1), drugmat2, '*'), c(row, col^2)))
}
.getCCIEntry = function (drugmat1, drugmat2) {
return(cbind((drugmat1 * drugmat2), (drugmat1 + drugmat2)))
}
.getCDIinner = function (a, b, f, ...) {
# For computing column-by-column (pseudo)-tensor product type interactions
f = match.fun(f)
apply(b, 2, function (x) apply(a, 1, function (y) f(x, y, ...)))
}
.getCDICombine = function (drugmat, DNAmat) {
return(cbind(drugmat, DNAmat))
}
.getCDITensor = function (drugmat, DNAmat, row, dcol, pcol) {
return(array(.getCDIinner(t(drugmat), DNAmat, '*'), c(row, dcol * pcol)))
}
#' @title Generating Interaction Descriptors
#'
#' @description Generating Interaction Descriptors
#'
#' @details This function calculates the interaction descriptors
#' by three types of interaction:
#' \itemize{
#' \item \code{combine} - combine the two descriptor matrix,
#' result has \code{(p1 + p2)} columns
#' \item \code{tensorprod} - calculate column-by-column
#' (pseudo)-tensor product type interactions, result has
#' \code{(p1 * p2)} columns
#' \item \code{entrywise} - calculate entrywise product and
#' entrywise sum of the two matrices, then combine them,
#' result has \code{(p + p)} columns
#' }
#'
#' @param drugmat The compound descriptor matrix.
#' @param protmat The protein descriptor matrix.
#' @param type The interaction type, one or more of
#' \code{"combine"}, \code{"tensorprod"}, and \code{"entrywise"}.
#'
#' @return A matrix containing the interaction descriptors
#'
#' @keywords getCPI getCDI getDPI getPPI getDDI getCCI interaction
#'
#' @aliases getCPI
#'
#' @author Min-feng Zhu <\email{wind2zhu@@163.com}>,
#' Nan Xiao <\url{http://r2s.name}>
#'
#' @export getCPI
#'
#' @examples
#' x = matrix(1:10, ncol = 2)
#' y = matrix(1:15, ncol = 3)
#' # getCPI
#' getCPI(x, y, 'combine')
#' # getCDI
#' getCDI(x, y, 'tensorprod')
#' # getDPI
#' getDPI(x, y, type = c('combine', 'tensorprod'))
#' getDPI(x, y, type = c('tensorprod', 'combine'))
#'
getCPI = function (drugmat, protmat, type = c('combine', 'tensorprod')) {
if (!is.matrix(drugmat)) drugmat = as.matrix(drugmat)
if (!is.matrix(protmat)) protmat = as.matrix(protmat)
drugrow = nrow(drugmat)
protrow = nrow(protmat)
if (drugrow != protrow) stop('Matrix row count must match')
drugcol = ncol(drugmat)
protcol = ncol(protmat)
if (missing(type)) stop('Must provide at least one interaction type')
if (all(type == 'combine')) {
result = .getCPICombine(drugmat, protmat)
} else if (all(type == 'tensorprod')) {
result = .getCPITensor(drugmat, protmat, row = drugrow,
dcol = drugcol, pcol = protcol)
} else if (length(setdiff(type, c('tensorprod', 'combine'))) == 0L) {
result = cbind(.getCPICombine(drugmat, protmat),
.getCPITensor(drugmat, protmat, row = drugrow,
dcol = drugcol, pcol = protcol))
} else {
stop('Interaction type must be in "tensorprod" and "combine" or both')
}
return(result)
}
#' @rdname getCPI
#'
#' @aliases getPPI
#'
#' @param protmat1 The first protein descriptor matrix,
#' must have the same ncol with \code{protmat2}.
#' @param protmat2 The second protein descriptor matrix,
#' must have the same ncol with \code{protmat1}.
#'
#' @export getPPI
#'
#' @examples
#' x = matrix(1:10, ncol = 2)
#' y = matrix(5:14, ncol = 2)
#'
#' # getPPI
#' getPPI(x, y, type = 'combine')
#' getPPI(x, y, type = 'tensorprod')
#' # getDDI
#' getDDI(x, y, type = 'entrywise')
#' getDDI(x, y, type = c('combine', 'tensorprod'))
#' # getCCI
#' getCCI(x, y, type = c('combine', 'entrywise'))
#' getCCI(x, y, type = c('entrywise', 'tensorprod'))
#' getCCI(x, y, type = c('combine', 'entrywise', 'tensorprod'))
getPPI = function (protmat1, protmat2, type = c('combine', 'tensorprod',
'entrywise')) {
if (!is.matrix(protmat1)) protmat1 = as.matrix(protmat1)
if (!is.matrix(protmat2)) protmat2 = as.matrix(protmat2)
protrow1 = nrow(protmat1)
protrow2 = nrow(protmat2)
if (protrow1 != protrow2) stop('Matrix row count must match')
protcol1 = ncol(protmat1)
protcol2 = ncol(protmat2)
if (protcol1 != protcol2) stop('Matrix column count must match')
if (missing(type)) stop('Must provide at least one interaction type')
if (all(type == 'combine')) {
result = .getPPICombine(protmat1, protmat2)
} else if (all(type == 'tensorprod')) {
result = .getPPITensor(protmat1, protmat2,
row = protrow1, col = protcol1)
} else if (all(type == 'entrywise')) {
result = .getPPIEntry(protmat1, protmat2)
} else if (length(setdiff(type, c('tensorprod', 'combine'))) == 0L) {
result = cbind(.getPPICombine(protmat1, protmat2),
.getPPITensor(protmat1, protmat2,
row = protrow1, col = protcol1))
} else if (length(setdiff(type, c('tensorprod', 'entrywise'))) == 0L) {
result = cbind(.getPPITensor(protmat1, protmat2,
row = protrow1,
col = protcol1),
.getPPIEntry(protmat1, protmat2))
} else if (length(setdiff(type, c('combine', 'entrywise'))) == 0L) {
result = cbind(.getPPICombine(protmat1, protmat2),
.getPPIEntry(protmat1, protmat2))
} else if (length(setdiff(type, c('tensorprod',
'combine',
'entrywise'))) == 0L) {
result = cbind(.getPPICombine(protmat1, protmat2),
.getPPITensor(protmat1, protmat2,
row = protrow1,
col = protcol1),
.getPPIEntry(protmat1, protmat2))
} else {
stop('Interaction type must be in "tensorprod", "combine" and "entrywise"')
}
return(result)
}
#' @rdname getCPI
#'
#' @aliases getDDI
#'
#' @param DNAmat1 The first DNA descriptor matrix,
#' must have the same ncol with \code{DNAmat2}.
#' @param DNAmat2 The second DNA descriptor matrix,
#' must have the same ncol with \code{DNAmat1}.
#'
#' @export getDDI
#'
getDDI = function (DNAmat1, DNAmat2, type = c('combine', 'tensorprod',
'entrywise')) {
if (!is.matrix(DNAmat1)) DNAmat1 = as.matrix(DNAmat1)
if (!is.matrix(DNAmat2)) DNAmat2 = as.matrix(DNAmat2)
DNArow1 = nrow(DNAmat1)
DNArow2 = nrow(DNAmat2)
if (DNArow1 != DNArow2) stop('Matrix row count must match')
DNAcol1 = ncol(DNAmat1)
DNAcol2 = ncol(DNAmat2)
if (DNAcol1 != DNAcol2) stop('Matrix column count must match')
if (missing(type)) stop('Must provide at least one interaction type')
if (all(type == 'combine')) {
result = .getDDICombine(DNAmat1, DNAmat2)
} else if (all(type == 'tensorprod')) {
result = .getDDITensor(DNAmat1, DNAmat2,
row = DNArow1, col = DNAcol1)
} else if (all(type == 'entrywise')) {
result = .getDDIEntry(DNAmat1, DNAmat2)
} else if (length(setdiff(type, c('tensorprod', 'combine'))) == 0L) {
result = cbind(.getDDICombine(DNAmat1, DNAmat2),
.getDDITensor(DNAmat1, DNAmat2,
row = DNArow1, col = DNAcol1))
} else if (length(setdiff(type, c('tensorprod', 'entrywise'))) == 0L) {
result = cbind(.getDDITensor(DNAmat1, DNAmat2,
row = DNArow1,
col = DNAcol1),
.getDDIEntry(DNAmat1, DNAmat2))
} else if (length(setdiff(type, c('combine', 'entrywise'))) == 0L) {
result = cbind(.getDDICombine(DNAmat1, DNAmat2),
.getDDIEntry(DNAmat1, DNAmat2))
} else if (length(setdiff(type, c('tensorprod',
'combine',
'entrywise'))) == 0L) {
result = cbind(.getDDICombine(DNAmat1, DNAmat2),
.getDDITensor(DNAmat1, DNAmat2,
row = DNArow1,
col = DNAcol1),
.getDDIEntry(DNAmat1, DNAmat2))
} else {
stop('Interaction type must be in "tensorprod", "combine" and "entrywise"')
}
return(result)
}
#' @rdname getCPI
#'
#' @aliases getDPI
#'
#' @param DNAmat The DNA descriptor matrix.
#'
#' @export getDPI
#'
getDPI = function (DNAmat, protmat, type = c('combine', 'tensorprod')) {
if (!is.matrix(DNAmat)) DNAmat = as.matrix(DNAmat)
if (!is.matrix(protmat)) protmat = as.matrix(protmat)
DNArow = nrow(DNAmat)
protrow = nrow(protmat)
if (DNArow != protrow) stop('Matrix row count must match')
DNAcol = ncol(DNAmat)
protcol = ncol(protmat)
if (missing(type)) stop('Must provide at least one interaction type')
if (all(type == 'combine')) {
result = .getDPICombine(DNAmat, protmat)
} else if (all(type == 'tensorprod')) {
result = .getDPITensor(DNAmat, protmat, row = DNArow,
dcol = DNAcol, pcol = protcol)
} else if (length(setdiff(type, c('tensorprod', 'combine'))) == 0L) {
result = cbind(.getDPICombine(DNAmat, protmat),
.getDPITensor(DNAmat, protmat, row = DNArow,
dcol = DNAcol, pcol = protcol))
} else {
stop('Interaction type must be in "tensorprod" and "combine" or both')
}
return(result)
}
#' @rdname getCPI
#'
#' @aliases getCCI
#'
#' @param drugmat1 The first compound descriptor matrix,
#' must have the same ncol with \code{drugmat2}.
#' @param drugmat2 The second compound descriptor matrix,
#' must have the same ncol with \code{drugmat1}.
#'
#' @export getCCI
#'
getCCI = function (drugmat1, drugmat2, type = c('combine', 'tensorprod',
'entrywise')) {
if (!is.matrix(drugmat1)) drugmat1 = as.matrix(drugmat1)
if (!is.matrix(drugmat2)) drugmat2 = as.matrix(drugmat2)
drugrow1 = nrow(drugmat1)
drugrow2 = nrow(drugmat2)
if (drugrow1 != drugrow2) stop('Matrix row count must match')
drugcol1 = ncol(drugmat1)
drugcol2 = ncol(drugmat2)
if (drugcol1 != drugcol2) stop('Matrix column count must match')
if (missing(type)) stop('Must provide at least one interaction type')
if (all(type == 'combine')) {
result = .getCCICombine(drugmat1, drugmat2)
} else if (all(type == 'tensorprod')) {
result = .getCCITensor(drugmat1, drugmat2,
row = drugrow1, col = drugcol1)
} else if (all(type == 'entrywise')) {
result = .getCCIEntry(drugmat1, drugmat2)
} else if (length(setdiff(type, c('tensorprod', 'combine'))) == 0L) {
result = cbind(.getCCICombine(drugmat1, drugmat2),
.getCCITensor(drugmat1, drugmat2,
row = drugrow1, col = drugcol1))
} else if (length(setdiff(type, c('tensorprod', 'entrywise'))) == 0L) {
result = cbind(.getCCITensor(drugmat1, drugmat2,
row = drugrow1,
col = drugcol1),
.getCCIEntry(drugmat1, drugmat2))
} else if (length(setdiff(type, c('combine', 'entrywise'))) == 0L) {
result = cbind(.getCCICombine(drugmat1, drugmat2),
.getCCIEntry(drugmat1, drugmat2))
} else if (length(setdiff(type, c('tensorprod',
'combine',
'entrywise'))) == 0L) {
result = cbind(.getCCICombine(drugmat1, drugmat2),
.getCCITensor(drugmat1, drugmat2,
row = drugrow1,
col = drugcol1),
.getCCIEntry(drugmat1, drugmat2))
} else {
stop('Interaction type must be in "tensorprod", "combine" and "entrywise"')
}
return(result)
}
#' @rdname getCPI
#'
#' @aliases getCDI
#'
#' @export getCDI
#'
getCDI = function (drugmat, DNAmat, type = c('combine', 'tensorprod')) {
if (!is.matrix(drugmat)) drugmat = as.matrix(drugmat)
if (!is.matrix(DNAmat)) DNAmat = as.matrix(DNAmat)
drugrow = nrow(drugmat)
DNArow = nrow(DNAmat)
if (drugrow != DNArow) stop('Matrix row count must match')
drugcol = ncol(drugmat)
DNAcol = ncol(DNAmat)
if (missing(type)) stop('Must provide at least one interaction type')
if (all(type == 'combine')) {
result = .getCDICombine(drugmat, DNAmat)
} else if (all(type == 'tensorprod')) {
result = .getCDITensor(drugmat, DNAmat, row = drugrow,
dcol = drugcol, pcol = DNAcol)
} else if (length(setdiff(type, c('tensorprod', 'combine'))) == 0L) {
result = cbind(.getCDICombine(drugmat, DNAmat),
.getCDITensor(drugmat, DNAmat, row = drugrow,
dcol = drugcol, pcol = DNAcol))
} else {
stop('Interaction type must be in "tensorprod" and "combine" or both')
}
return(result)
}
Try the BioMedR package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.