This function determines the patterns between different
conditions of each gene. It should be applied to the output of
calculate_condition_mean_sd_per_gene.
Arguments
- tbl
the output of
calculate_condition_mean_sd_per_gene- n_sd
number of standard deviations from the mean to use to construct the intervals; default is 2
Value
A matrix of single character patterns between conditions. The last column is named pattern and is a concatenation of all other columns.
Examples
expression.matrix.preproc <- as.matrix(read.csv(
system.file("extdata", "expression_matrix_preprocessed.csv", package = "bulkAnalyseR"),
row.names = 1
))[1:500,]
condition <- factor(rep(c("0h", "12h", "36h"), each = 2))
tbl <- calculate_condition_mean_sd_per_gene(expression.matrix.preproc[1:10, ], condition)
#>
|
| | 0%
|
|======================================================================| 100%
patmat <- make_pattern_matrix(tbl)
#>
|
| | 0%
|
|======================================================================| 100%
patmat
#> 0h -> 12h 12h -> 36h pattern
#> ENSMUSG00000025902 "S" "S" "SS"
#> ENSMUSG00000098104 "S" "S" "SS"
#> ENSMUSG00000103922 "S" "S" "SS"
#> ENSMUSG00000033845 "U" "S" "US"
#> ENSMUSG00000102275 "S" "S" "SS"
#> ENSMUSG00000025903 "S" "S" "SS"
#> ENSMUSG00000033813 "S" "S" "SS"
#> ENSMUSG00000002459 "S" "S" "SS"
#> ENSMUSG00000085623 "S" "S" "SS"
#> ENSMUSG00000033793 "D" "U" "DU"