Calculate statistics for each gene of an expression matrix given a grouping
Source:R/patternFuns.R
calculate_condition_mean_sd_per_gene.RdThis function calculates the mean and standard deviation of the expression of each gene in an expression matrix, grouped by the conditions supplied.
Arguments
- expression.matrix
the expression matrix; rows correspond to genes and columns correspond to samples; usually preprocessed by
preprocessExpressionMatrix; a list (of the same length as modality) can be provided if #'length(modality) > 1- condition
the condition to group the columns of the expression matrix by; must be a factor of the same length as ncol(expression.matrix)
Value
A tibble in long format, with the mean and standard deviation of each gene in each condition. The standard deviation is increased to the minimum value in the expression matrix (the noise threshold) if it is lower, in order to avoid sensitivity to small changes.
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)
#>
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|======================================================================| 100%
tbl
#> # A tibble: 30 x 4
#> gene condition mean sd
#> <chr> <fct> <dbl> <dbl>
#> 1 ENSMUSG00000025902 0h 106. 45.7
#> 2 ENSMUSG00000025902 12h 60.8 45.7
#> 3 ENSMUSG00000025902 36h 60.2 45.7
#> 4 ENSMUSG00000098104 0h 95.8 45.7
#> 5 ENSMUSG00000098104 12h 86.1 45.7
#> 6 ENSMUSG00000098104 36h 78 45.7
#> 7 ENSMUSG00000103922 0h 281. 45.7
#> 8 ENSMUSG00000103922 12h 376. 48.4
#> 9 ENSMUSG00000103922 36h 315. 45.7
#> 10 ENSMUSG00000033845 0h 10868. 933.
#> # ... with 20 more rows