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Transform Phylostratum Values

Source: R/tfPS.R
tfPS.Rd

This function performs transformation of phylostratum values.

Usage

tfPS(ExpressionSet, transform)

Arguments

ExpressionSet

a standard PhyloExpressionSet object.

transform

a character vector of any valid function that transforms PS values. Possible values can be:

  • transform = "qr" (or "quantilerank") : quantile rank transformation analogous to Julia function StatsBase.quantilerank using method = :tied.

Value

a standard PhloExpressionSet object storing transformed Phylostratum levels.

Details

This function transforms the phylostratum assignment. The return value of this function is a PhyloExpressionSet object with transformed phylostratum tfPhylostratum as the first column, satisfying is.ExpressionSet. Note that the input transform must be an available function, currently limited to only "qr" (or "quantilerank").

See also

tf

Author

Jaruwatana Sodai Lotharukpong and Lukas Maischak

Examples

# source the example dataset
data(PhyloExpressionSetExample)
 
# get the relative expression profiles for each phylostratum
tfPES <- tfPS(PhyloExpressionSetExample, transform = "qr")
head(tfPES)
#>   tfPhylostratum      GeneID     Zygote   Quadrant   Globular      Heart
#> 1      0.1801861 at1g01040.2  2173.6352  1911.2001  1152.5553  1291.4224
#> 2      0.1801861 at1g01050.1  1501.0141  1817.3086  1665.3089  1564.7612
#> 3      0.1801861 at1g01070.1  1212.7927  1233.0023   939.2000   929.6195
#> 4      0.1801861 at1g01080.2  1016.9203   936.3837  1181.3381  1329.4734
#> 5      0.1801861 at1g01090.1 11424.5667 16778.1685 34366.6493 39775.6405
#> 6      0.1801861 at1g01120.1   844.0414   787.5929   859.6267   931.6180
#>      Torpedo       Bent    Mature
#> 1  1000.2529   962.9772 1696.4274
#> 2  1496.3207  1114.6435 1071.6555
#> 3   864.2180   877.2060  894.8189
#> 4  1392.6429  1287.9746  861.2605
#> 5 56231.5689 66980.3673 7772.5617
#> 6   942.8453   870.2625  792.7542