CODEWITHSUNDEEP
raggregate
prog2de
prog2de

Reputation: 329

What does aggregate do here?

I have a R script with following line:

KSData.dataset.abbrev = aggregate(log2FC ~ Kinase.Gene+Substrate.Gene+Substrate.Mod+Source, data=KSData.dataset.abbrev, FUN=mean)

KSData.dataset.abbrev looks like this:

    Kinase.Gene Substrate.Gene Substrate.Mod                          Peptide           p        FC       log2FC          Source
364        ABL1          RBM39           Y95                        YRSPYSGPK 0.019590948 1.6158045  0.692252615 PhosphoSitePlus
8          AKT1         AKT1S1          T246                         LNTSDFQK 0.800879536 0.8909224 -0.166628324 PhosphoSitePlus
121        AKT1          EPHA2          S897                    LPSTSGSEGVPFR 0.500658346 0.7052020 -0.503891606 PhosphoSitePlus

after using the code line above, the df looks similar to this:

    Kinase.Gene Substrate.Gene Substrate.Mod          Source        log2FC
430        ABL1          RBM39           Y95 PhosphoSitePlus  0.6922526152
19         AKT1          PEA15          S116 PhosphoSitePlus  1.1782441053
80         AKT1           MDM2          S166 PhosphoSitePlus -0.7967537534

I have no clue, what exaclty this line do... Thanks for any help

Upvotes: 0

Views: 43

Answers (1)

GKi
GKi

Reputation: 39657

I calculates the mean of log2FC for the unique groups combinations Kinase.Gene, Substrate.Gene, Substrate.Mod and Source.

Using a small data sample, you can see what aggregate is doing:

(tt  <- data.frame(a = 1:2, b=1:3, x=1:12))
#   a b  x
#1  1 1  1
#2  2 2  2
#3  1 3  3
#4  2 1  4
#5  1 2  5
#6  2 3  6
#7  1 1  7
#8  2 2  8
#9  1 3  9
#10 2 1 10
#11 1 2 11
#12 2 3 12

aggregate(x ~ a, data=tt, FUN=mean) #Average for the groups in col a
#  a x
#1 1 6
#2 2 7

aggregate(x ~ a + b, data=tt, FUN=mean) #Average for the groups in col a and b
#  a b x
#1 1 1 4
#2 2 1 7
#3 1 2 8
#4 2 2 5
#5 1 3 6
#6 2 3 9

Upvotes: 1

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