pickgene-internal          package:pickgene          R Documentation

_I_n_t_e_r_n_a_l _p_i_c_k_g_e_n_e _f_u_n_c_t_i_o_n_s.

_D_e_s_c_r_i_p_t_i_o_n:

     These are generally not to be called by the user.

_U_s_a_g_e:

     adjustlevel(ntest, alpha)
     chen.poly(cv, err)
     chipnorm(xx, chip)
     dencont(x, y, align, crit, xlim, ylim, dolog, byranks, dif,
                      ave, numlines, levels.z)
     dencum(x, y, align, crit, xlim, ylim, dolog, byranks,
                      standardize, dif, ave, splineit, numlines, show,
                      levels.z)
     denlines(x, y, align, crit, xlim, ylim, dolog, dif, ave,
                      numlines, offset)
     do.oddsplot(data, main, theta, col, redo, conditions, identifier,
                      ...)
     fitgg(xx, yy, start)
     gammaden(x, a, b)
     holms(x, alpha, cut)
     lod.ggb(x, y, theta)
     lod.plot(data, x, y, theta, filename, probe, xlab, ylab, ps,
                      col, lowlod, ...)
     lodprobes(xx, yy, theta, lod, probes, col, lowlod, offset)
     loglik(theta, xx, yy)
     makecont(x, y, size, cex, levels)
     multipickgene(...)
     nlminb(start, objective, lower, xx, yy, zz, use.optim)
     nloglik(theta, xx, yy)
     normal.richmond(foo, channel)
     npdiag(xx, yy, aa, a0, nu, pp)
     nploglik(theta, xx, yy, zz)
     orangene(n, center, spread, contamination, alpha, noise,
                      omega)
     pickedchisq(pick, show, title, plotit, alpha)
     pickedhist(pick, show, title, p1, plotit, rotate, mfrow, bw)
     pickedpair(x, columns, description, probe, renorm, pick, main,
                      ...)
     pickedscore(pick, description, show, alpha, xlab, ylab, main,
                      mfrow)
     pickgene2(...)
     pickgene.poly(x, condi, geneID, overalllevel, npickgene, d, ylabs,
                      contrastnames, ...)
     pickgene.two(y, intensity, geneid, singlelevel, npickgene,
                      meanrank, xlab, ylab, main, plotit, col, negative,
                      ...)
     pmarg(xx, yy, theta, nsupp)
     predrecur(xx, theta, gridlim)
     rangene(n, center, spread, contamination, alpha, noise,
                      omega)
     rankgene(xx, yy, fits)
     robustbox(y, x, nslice, xlab, ylab, shrink, crit, overalllevel,
                      cex, lwd, plotit)
     s.check0(xx, yy, theta1, theta2, chip)
     s.check1(xx, yy, theta, chip)
     s.check2(foo, xa, ya, thetaa, xb, yb, thetab, spots)
     shrinkplot(xx, yy, fits, chip)
     sixden(x, y, align, crit, xlim, dolog, dif, ave)
     s.marg(xx, yy, aa, a0, nuA, nu0, p)
     toprankgene(yy, n)
     twoarray.norm(foo, ..., conditions, reduce, identifier)
     twoarray.plot(mydata, main, theta, conditions, identifier)
     twowayanovapickgene(x, fac1level, fac2level, ...)

_A_u_t_h_o_r(_s):

     Brian S. Yandell, yandell@stat.wisc.edu

