This function takes an ExpressionSet object storing either a constant or variable number
of biological or technical replicates per stage and collapses replicate expression levels using a defined FUN (window function).
CollapseReplicates(ExpressionSet, nrep, FUN, stage.names = NULL)a standard PhyloExpressionSet or DivergenceExpressionSet object.
either a numeric value specifying the constant number of replicates per stage or a numeric vector specifying the variable number of replicates for each stage position.
a window function (e.g., mean, median, max, min, etc.) specifying how replicate expression levels should be collapsed.
a character vector specifying the new names of collapsed stages.
data(PhyloExpressionSetExample)
# combine the expression levels of the 2 replicates (const) per stage
# using mean as window function and rename new stages: "S1","S2","S3"
CollapseReplicates(ExpressionSet = PhyloExpressionSetExample[1:5,1:8],
nrep = 2,
FUN = mean,
stage.names = c("S1","S2","S3"))
#> # A tibble: 5 × 5
#> Phylostratum GeneID S1 S2 S3
#> <int> <fct> <dbl> <dbl> <dbl>
#> 1 1 at1g01040.2 2042. 1222. 982.
#> 2 1 at1g01050.1 1659. 1615. 1305.
#> 3 1 at1g01070.1 1223. 934. 871.
#> 4 1 at1g01080.2 977. 1255. 1340.
#> 5 1 at1g01090.1 14101. 37071. 61606.
# combine the expression levels of the 2 replicates (stage one), 2 replicates (stage two),
# and 3 replicates (stage three) using mean as window function
# and rename new stages: "S1","S2","S3"
CollapseReplicates(ExpressionSet = PhyloExpressionSetExample[1:5,1:9],
nrep = c(2,2,3),
FUN = mean,
stage.names = c("S1","S2","S3"))
#> # A tibble: 5 × 5
#> Phylostratum GeneID S1 S2 S3
#> <int> <fct> <dbl> <dbl> <dbl>
#> 1 1 at1g01040.2 2042. 1222. 1220.
#> 2 1 at1g01050.1 1659. 1615. 1228.
#> 3 1 at1g01070.1 1223. 934. 879.
#> 4 1 at1g01080.2 977. 1255. 1181.
#> 5 1 at1g01090.1 14101. 37071. 43661.