Nothing
## ---- echo = FALSE, message = FALSE---------------------------------------------------------------
library(markdown)
library(knitr)
knitr::opts_chunk$set(
error = FALSE,
tidy = FALSE,
message = FALSE,
fig.align = "center")
options(width = 100)
options(rmarkdown.html_vignette.check_title = FALSE)
library(cola)
## ---- eval = FALSE--------------------------------------------------------------------------------
# ind = sample(ncol(mat), 200)
# mat1 = mat[, ind]
## ---- eval = FALSE--------------------------------------------------------------------------------
# rl = run_all_consensus_partition_methods(mat1, ...)
# cola_report(rl, ...)
## ---- eval = FALSE--------------------------------------------------------------------------------
# res = consensus_partition(mat, top_value_method = tm, partition_method = pm, ...)
## ---- eval = FALSE--------------------------------------------------------------------------------
# res = rl[tm, pm]
## ---- eval = FALSE--------------------------------------------------------------------------------
# mat2 = mat[, setdiff(seq_len(ncol(mat)), ind)]
# mat2 = t(scale(t(mat2)))
# cl = predict_classes(res, mat2)
## ---- eval = FALSE--------------------------------------------------------------------------------
# cl = predict_classes(res, t(scale(t(mat))))
## ---- eval = FALSE--------------------------------------------------------------------------------
# data(golub_cola)
# m = get_matrix(golub_cola)
#
# set.seed(123)
# golub_cola_ds = consensus_partition_by_down_sampling(m, subset = 50,
# anno = get_anno(golub_cola), anno_col = get_anno_col(golub_cola),
# top_value_method = "SD", partition_method = "kmeans")
## -------------------------------------------------------------------------------------------------
data(golub_cola_ds)
golub_cola_ds
## -------------------------------------------------------------------------------------------------
class = get_classes(golub_cola_ds, k = 2)
nrow(class)
class
## -------------------------------------------------------------------------------------------------
get_classes(golub_cola_ds, p_cutoff = 0.05)
## ---- fig.width = 8, fig.height = 7, out.width = "500"--------------------------------------------
dimension_reduction(golub_cola_ds, k = 2)
## ---- fig.width = 8, fig.height = 7, out.width = "500"--------------------------------------------
get_signatures(golub_cola_ds, k = 2)
## -------------------------------------------------------------------------------------------------
sessionInfo()
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