HenrikBengtsson / hsa

Non-Official Fork: Integrating Multi-Track Hi-C Data for Genome-Scale Reconstruction of 3D Chromatin Structure
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ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [rbind] #2

Open HenrikBengtsson opened 4 years ago

HenrikBengtsson commented 4 years ago

[deleted]

HenrikBengtsson commented 4 years ago

None of the cbind() methods do stringsAsFactors coercions, which leaves:

$ echo "$pkg:"; (cd "$pkg"; grep -E "^[ \t]*[^#].*rbind" -- */*.R | grep -vF stringsAsFactors;)
hsa:
R/cstruct1.R:    p0 - rbind(p0[-1, ] * rho, zeros_3) - rbind(zeros_3, p0[-N, ] * rho)
R/cstruct1.R:    Y <- rbind(S0_c35, rnorm(3, mean = S0_c35[n, ], sd = colSds(S0_c35[-1, ] - S0_c35[-n, ])))
R/cstruct1.R:  P <- rbind(P0[index[1, 1]:index[1, 2], -1], do.call(rbind, args = sapply2(2:dim(index)[1], FUN = function(x) {
R/cstruct1.R:  P <- rbind(P0[index[1, 1]:index[1, 2], -1], do.call(rbind, args = sapply2(2:dim(index)[1], FUN = function(x) {
R/cstruct1.R:      fL(cbind(pbin_t, rbind(q0, q)), A, b, invSigma, beta, cx_t, mat_t)
R/cstruct1.R:    return(rbind(q0, t(Padd[["par"]])))
R/cstruct1.R:      fL(cbind(pbin_t, rbind(temp, q)), A, b, invSigma, beta, cx_t, mat_t)
R/cstruct1.R:    return(rbind(temp, t(Padd[["par"]])))
R/cstruct1.R:      fL(cbind(pbin_t, rbind(temp_t, x)), A, b, invSigma, beta, cx_t, mat_t)
R/cstruct1.R:    return(rbind(temp, t(addq)))
R/cstruct1.R:  -floglike(cbind(pbin, rbind(P1, t(t(P2 %*% theta[-4, ]) + theta[4, ]))), A0, b0, invSigma0, beta1, covmat0, mat)
R/finital.R:      theta <- optim(as.vector(rbind(diag(3), P[index[i - 1, 2], ] - P[index_ri_c1, ] + rnorm(3L, sd = 1/100))), fn = function(x) {
R/fmain.R:    bin <- rbind(bin, lsmap0[[i]][, 1:2])
R/fmain.R:    Psub <- do.call(rbind, args = lapply(1:dim(index)[1], FUN = function(x) {
R/fmain.R:      Psub <- do.call(rbind, args = lapply(1:dim(index)[1], FUN = function(x) {
R/utils.R:  base_rbind <- base::rbind
R/utils.R:  function(...) base_rbind(..., deparse.level = 0L)