get_signatures-DownSamplingConsensusPartition-method {cola} | R Documentation |
Get signature rows
## S4 method for signature 'DownSamplingConsensusPartition' get_signatures(object, k, p_cutoff = 0.05, fdr_cutoff = cola_opt$fdr_cutoff, group_diff = cola_opt$group_diff, scale_rows = object@scale_rows, row_km = NULL, diff_method = c("Ftest", "ttest", "samr", "pamr", "one_vs_others"), anno = get_anno(object), anno_col = get_anno_col(object), internal = FALSE, show_row_dend = FALSE, show_column_names = FALSE, use_raster = TRUE, plot = TRUE, verbose = TRUE, seed = 888, left_annotation = NULL, right_annotation = NULL, col = if(scale_rows) c("green", "white", "red") else c("blue", "white", "red"), simplify = FALSE, ...)
object |
A |
k |
Number of subgroups. |
p_cutoff |
Cutoff for p-values of class label prediction. Samples with values higher than it are not used for finding signature rows. |
fdr_cutoff |
Cutoff for FDR of the difference test between subgroups. |
group_diff |
Cutoff for the maximal difference between group means. |
scale_rows |
Whether apply row scaling when making the heatmap. |
row_km |
Number of groups for performing k-means clustering on rows. By default it is automatically selected. |
diff_method |
Methods to get rows which are significantly different between subgroups, see 'Details' section. |
anno |
A data frame of annotations for the original matrix columns. By default it uses the annotations specified in |
anno_col |
A list of colors (color is defined as a named vector) for the annotations. If |
internal |
Used internally. |
show_row_dend |
Whether show row dendrogram. |
show_column_names |
Whether show column names in the heatmap. |
use_raster |
Internally used. |
plot |
Whether to make the plot. |
verbose |
Whether to print messages. |
seed |
Random seed. |
left_annotation |
Annotation put on the left of the heatmap. It should be a |
right_annotation |
Annotation put on the right of the heatmap. Same format as |
col |
Colors. |
simplify |
Only use internally. |
... |
Other arguments. |
This function is very similar as get_signatures,ConsensusPartition-method
.
data(golub_cola_ds) get_signatures(golub_cola_ds, k = 2) get_signatures(golub_cola_ds, k = 3)