r - Label list of data-frame based on filtering criteria

Question

list_of_files <- list.files('C1_to_C6/',pattern = '\.txt$', full.names = TRUE)

#Further arguments to read.csv can be passed in ...
all_csv <- lapply(list_of_files,read.csv)

#Set the name of each list element to its
names(all_csv) <- gsub(".txt","",
                       list.files("C1_to_C6/",full.names = FALSE),
                       fixed = TRUE)

The above code reads all my files into the list.

Now i have a list of data frame as such

list_of_files
 [1] "C1_to_C6//C1_C2_contrast.txt" "C1_to_C6//C1_C3_contrast.txt" "C1_to_C6//C1_C4_contrast.txt" "C1_to_C6//C1_C5_contrast.txt"
 [5] "C1_to_C6//C1_C6_contrast.txt" "C1_to_C6//C2_C3_contrast.txt" "C1_to_C6//C2_C4_contrast.txt" "C1_to_C6//C2_C5_contrast.txt"
 [9] "C1_to_C6//C2_C6_contrast.txt" "C1_to_C6//C3_C4_contrast.txt" "C1_to_C6//C3_C5_contrast.txt" "C1_to_C6//C4_C5_contrast.txt"
[13] "C1_to_C6//C4_C6_contrast.txt" "C1_to_C6//C5_C6_contrast.txt" "C1_to_C6//C6_C5_contrast.txt"

The genral structure of my data frame is like this, I was not able to put the dput of the dataframe as due to some issue whenever i do dput(head(a,5)) the whole data comes up

ab <- read.table(text = "
gene  baseMean log2FoldChange      lfcSE       stat       pvalue         padj
 ENSMUSG00000033845 1104.8298     0.30429069 0.06539399  4.6531907 3.268377e-06 4.019525e-05
 ENSMUSG00000025903  848.4143     0.13443658 0.07048958  1.9071837 5.649680e-02 1.440507e-01
 ENSMUSG00000033813  510.3910     0.05108741 0.09050085  0.5644965 5.724163e-01 7.234561e-01
 ENSMUSG00000033793 1569.8826     0.04845688 0.06197695  0.7818531 4.343009e-01 6.049862e-01
 ENSMUSG00000025907 1430.4057    -0.32015475 0.06772883 -4.7270084 2.278518e-06 2.924837e-05", header = TRUE)

To filter the single dataframe i do this.

sig_table_hw_oe <- filter(a, padj < 0.05 & abs(log2FoldChange) > 1)
UP_DOWN <- mutate(sig_table_hw_oe, UP_DOWN = ifelse(log2FoldChange > 1, "UP", "DOWN"))

Now i would like to do the same for the list of dataframe which i do for the single dataframe how to do it?

The output for single dataframe would be like this

gene  baseMean log2FoldChange     lfcSE      stat       pvalue         padj UP_DOWN
 ENSMUSG00000103509  18.57491      -3.194136 0.7446761 -4.289297 1.792399e-05 1.812452e-04    DOWN
 ENSMUSG00000104358  22.75726      -1.448193 0.5525529 -2.620913 8.769460e-03 3.439516e-02    DOWN
 ENSMUSG00000026069 525.12341       1.083185 0.1057836 10.239630 1.317393e-24 2.045214e-22      UP

This is what i want to achive for my list of data-frame and write them as output into a file.

UPDATE

Im able to apply the condition

abc <- lapply(all_csv, function(x) filter(x, padj < 0.05 & abs(log2FoldChange) > 1))

The above one filters my list of DF.

But when i try to label it using the below code I get the error as such

abd <- lapply(abc, function(x) filter(x, UP_DOWN = ifelse(log2FoldChange > 1, "UP", "DOWN")))

Error: Problem with `filter()` input `..1`.
x Input `..1` is named.
? This usually means that you've used `=` instead of `==`.
? Did you mean `UP_DOWN == ifelse(log2FoldChange > 1, "UP", "DOWN")`?
Run `rlang::last_error()` to see where the error occurred.  

Any suggestion how to do the above would be really appreciated.

question from:https://stackoverflow.com/questions/65861249/label-list-of-data-frame-based-on-filtering-criteria

Answer 1

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