r - How to preserve base data frame rownames upon filtering in dplyr chain

Question

I have the following data frame:

df <- structure(list(BoneMarrow = c(30, 0, 0, 31138, 2703), Pulmonary = c(3380, 
21223.3333333333, 0, 0, 27)), row.names = c("ATP1B1", "CYCS", 
"DDX5", "GNB2L1", "PRR11"), class = "data.frame", .Names = c("BoneMarrow", 
"Pulmonary"))

df 
#>        BoneMarrow Pulmonary
#> ATP1B1         30   3380.00
#> CYCS            0  21223.33
#> DDX5            0      0.00
#> GNB2L1      31138      0.00
#> PRR11        2703     27.00

What I want to do is to get rid of rows with values < 8 in any of the columns. I tried this but the row names (e.g. ATP1B1, CYCS etc) are gone:

> df %>% filter(!apply(., 1, function(row) any(row <= 8 )))
  BoneMarrow Pulmonary
1         30      3380
2       2703        27

How can I preserve that in dplyr chain?

Answer 1

you can convert rownames to a column and revert back after filtering:

library(dplyr)
library(tibble)  # for `rownames_to_column` and `column_to_rownames`

df %>%
    rownames_to_column('gene') %>%
    filter_if(is.numeric, all_vars(. >= 8)) %>%
    column_to_rownames('gene')

#        BoneMarrow Pulmonary
# ATP1B1         30      3380
# PRR11        2703        27