Average the replicates in a Spectra object and return a new Spectra object
with fewer samples. One should probably not do this until each individual sample has been
visualized for quality control, in case it is a potential outlier.
averageReplicates(spectra, uniq)An object of S3 class Spectra().
Character. A character vector containing strings representing unique sample
identifiers. The sample names will be searched for these strings, and all samples
matching a given string will be averaged and put into a new Spectra object. For
example, consider the case where samples are named
S_1_01, S_1_02, ..., S_2_01, S_2_02, ...
where _01 and so forth signifies replicates of a particular sample.
With uniq = c("S_1", "S_2") all S_1 replicates will be averaged and
all S_2 replicates will be averaged. N.B. the strings will be used as
regex pattern and grepped.
An object of S3 class Spectra.
data(SrE.IR)
averaged <- averageReplicates(SrE.IR, uniq = c("EPO", "OO", "adSrE", "pSrE"))
sumSpectra(SrE.IR)
#>
#> Serenoa repens IR quality study
#>
#> There are 16 spectra in this set.
#> The y-axis unit is absorbance.
#>
#> The frequency scale runs from
#> 399.2123 to 3999.837 wavenumber
#> There are 1868 frequency values.
#> The frequency resolution is
#> 1.9286 wavenumber/point.
#>
#>
#> The spectra are divided into 4 groups:
#>
#> group no. color symbol alt.sym
#> 1 adSrE 10 #984EA3 15 d
#> 2 EPO 1 #377EB8 2 b
#> 3 OO 1 #4DAF4A 3 c
#> 4 pSrE 4 #E41A1C 1 a
#>
#>
#> *** Note: this is an S3 object
#> of class 'Spectra'
sumSpectra(averaged)
#>
#> Serenoa repens IR quality study (replicates averaged)
#>
#> There are 4 spectra in this set.
#> The y-axis unit is absorbance.
#>
#> The frequency scale runs from
#> 399.2123 to 3999.837 wavenumber
#> There are 1868 frequency values.
#> The frequency resolution is
#> 1.9286 wavenumber/point.
#>
#>
#> The spectra are divided into 4 groups:
#>
#> group no. color symbol alt.sym
#> 1 EPO 1 #377EB8 2 b
#> 2 OO 1 #4DAF4A 3 c
#> 3 adSrE 1 #984EA3 15 d
#> 4 pSrE 1 #E41A1C 1 a
#>
#>
#> *** Note: this is an S3 object
#> of class 'Spectra'