数据框 R 列表的 lapply 和聚合列

Question

Newbie here, Thanks in advance for the help

I have a list of multiple dataframes (AllExplants), with the same number of columns (with identical names) and different number of rows. I wish to aggregate columns for all the dataframes in the list at once.

My data: I will use a list of two dataframes here for simplicity

AllExplants <- list(Explant1, Explant2)

Explant1:

 `Sample Name`                       `Tissue Category` `Annotation ID`                              All Negative `Non-nuclear`   PD1  PDL1
1 LT181- PD1 PDL1 MNF -1_Scan1.qptiff All               LT181- PD1 PDL1 MNF -1_Scan1_[10311,49192] 25140     4954            23  4418 15635
2 LT181- PD1 PDL1 MNF -1_Scan1.qptiff Stroma            LT181- PD1 PDL1 MNF -1_Scan1_[10311,49192]  8788     1678            23  2922  4114
3 LT181- PD1 PDL1 MNF -1_Scan1.qptiff Tumour            LT181- PD1 PDL1 MNF -1_Scan1_[10311,49192] 16344     3268             0  1496 11521
4 LT181- PD1 PDL1 MNF -1_Scan1.qptiff All               LT181- PD1 PDL1 MNF -1_Scan1_[10311,51272] 37930     9847           137  9821 17921
5 LT181- PD1 PDL1 MNF -1_Scan1.qptiff Stroma            LT181- PD1 PDL1 MNF -1_Scan1_[10311,51272] 17400     5700           123  4914  6544
6 LT181- PD1 PDL1 MNF -1_Scan1.qptiff Tumour            LT181- PD1 PDL1 MNF -1_Scan1_[10311,51272] 20526     4144            13  4907 11377
7 LT181- PD1 PDL1 MNF -1_Scan1.qptiff All               LT181- PD1 PDL1 MNF -1_Scan1_[12161,50230]  2315     1105            34   334   818
8 LT181- PD1 PDL1 MNF -1_Scan1.qptiff Stroma            LT181- PD1 PDL1 MNF -1_Scan1_[12161,50230]  1666      934            30   266   427
9 LT181- PD1 PDL1 MNF -1_Scan1.qptiff Tumour            LT181- PD1 PDL1 MNF -1_Scan1_[12161,50230]   639      164             1    68   391    

Explant2:

  `Sample Name`                       `Tissue Category` `Annotation ID`                              All Negative `Non-nuclear`   PD1  PDL1
1 LT181- PD1 PDL1 MNF -1_Scan1.qptiff All               LT181- PD1 PDL1 MNF -1_Scan1_[10872,46112] 19602     4370            47  3176 11983
2 LT181- PD1 PDL1 MNF -1_Scan1.qptiff Stroma            LT181- PD1 PDL1 MNF -1_Scan1_[10872,46112]  8479     2158            36  2624  3644
3 LT181- PD1 PDL1 MNF -1_Scan1.qptiff Tumour            LT181- PD1 PDL1 MNF -1_Scan1_[10872,46112] 11116     2207            11   552  8339
4 LT181- PD1 PDL1 MNF -1_Scan1.qptiff All               LT181- PD1 PDL1 MNF -1_Scan1_[11335,47845] 14783     2036            10  1697 10973
5 LT181- PD1 PDL1 MNF -1_Scan1.qptiff Stroma            LT181- PD1 PDL1 MNF -1_Scan1_[11335,47845]  3179      494             6   894  1770
6 LT181- PD1 PDL1 MNF -1_Scan1.qptiff Tumour            LT181- PD1 PDL1 MNF -1_Scan1_[11335,47845] 11604     1542             4   803  9203

I wish to aggregate columns 4-8 (ie All, Negative, Non-nuclear ,PD1 ,PDL1) and do so according to column 2 (Tissue Category)

I can do this for each individual dataframe (if it is not in a list), with the code below

Explant1_agg <- aggregate(Explant1 [,4:8], by=list(Explant1$`Tissue Category`), FUN=sum)

However that's time consuming, to apply the same function to all the dataframes in the list, I have tried this code, having looked at posts here:

AllExplants_agg <- lapply(AllExplants, function(x) {aggregate(x[,4:8], by=list(x[,2]),  FUN=sum)})

However R returns the error

 Error in aggregate.data.frame(x[, 4:8], by = list(x[, 2]), FUN = sum) : 
  arguments must have same length 

Any help would be greatly appreciated!

Answer 1

I know this question is already old, but I encountered the same problem and fixed it, and I thought it might still be of interest.
I didn't manage to get R to use a list in aggregate, but I worked around it with a for-loop:

dat=seq(from=1, by=1, to=length(All_Explants))
#list to ID dataframes
output_All_Explants=list() #create list for output data from for loop
for (i in dat) { 
    dummy=as.data.frame(All_Explants[[i]])
    Output_All_Explants[[i]]=aggregate(dummy[,4:8], 
    by=list(date=dummy$Tissue Category), FUN=sum) 
}