CODEWITHSUNDEEP
rfilterdplyr
DN1
DN1

Reputation: 218

How to address Error: Problem with `filter()` input `..1` with between function error?

I have code I run which is filtering grouped rows so only 1 row is left per group unless multiple rows pass all my filters. This code has already worked fine yesterday. However, today I used downloaded some new packages (that are for analyzing gene enrichment), and since using those my filtering code now gives me a new error:

SD1<- df %>% 
  group_by(group) %>% 
  filter(if(n() > 1) {(Score > SD) } else TRUE) %>%
  slice_max(count1, n = 1) %>% 
  slice_max(count2, n = 1) 

PPI <- df %>% 
  group_by(group) %>% 
  dplyr::filter(if(n() > 1) {(Score < SD) } else TRUE) %>%
  dplyr::filter(dplyr::between(Score, Average, SD)) %>%
  slice_max(count1, n = 1) %>% 
  slice_max(count2, n = 1) %>% 
  subset(!(group %in% SD1$group)) %>%
  ungroup()

Error: Problem with `filter()` input `..1`.
x `left` must be length 1
i Input `..1` is `dplyr::between(Score, Average, SD)`.
i The error occurred in group 1: group = 1.

I've seen similar questions but trying to apply their answers hasn't worked in my use-case.

Is there a coding reason why this has appeared or is it a problem dplyr is having with a new conflicting package I've installed in RStudio? It's the only thing I've done differently that I know of.

The data it is filtering looks like:

group       gene       Score       Average       SD   count1 count2 
1           gene1        0.1                   0.43               0.75                 0                 1
1           gene2        0.5                   0.43               0.75                 0                23
1           gene3        0.7                   0.43               0.75                 1                45
2           gene4        0.88                  0.7                0.75

Session info:

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.5.1     stringr_1.4.0     purrr_0.3.4       readr_1.4.0       tibble_3.0.6     
 [6] ggplot2_3.3.3     tidyverse_1.3.0   tidyr_1.1.2       dplyr_1.0.3       data.table_1.13.6

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6        pillar_1.4.7      compiler_4.0.2    cellranger_1.1.0  dbplyr_2.0.0     
 [6] tools_4.0.2       jsonlite_1.7.2    lubridate_1.7.9.2 lifecycle_0.2.0   gtable_0.3.0     
[11] pkgconfig_2.0.3   rlang_0.4.10      reprex_1.0.0      cli_2.3.0         rstudioapi_0.13  
[16] DBI_1.1.1         haven_2.3.1       withr_2.4.1       xml2_1.3.2        httr_1.4.2       
[21] fs_1.5.0          generics_0.1.0    vctrs_0.3.6       hms_1.0.0         grid_4.0.2       
[26] tidyselect_1.1.0  glue_1.4.2        R6_2.5.0          readxl_1.3.1      modelr_0.1.8     
[31] magrittr_2.0.1    backports_1.2.1   scales_1.1.1      ellipsis_0.3.1    rvest_0.3.6      
[36] assertthat_0.2.1  colorspace_2.0-0  stringi_1.5.3     munsell_0.5.0     broom_0.7.4      
[41] crayon_1.4.0

Upvotes: 2

Views: 4573

Answers (1)

akrun
akrun

Reputation: 887511

The error occurred in the last step of subset (in tidyverse, it would be with filter) though as "UpperSD_Genes" dataset shows 0 rows and thus it is not able to extract values from that column

nrow(UpperSD_Genes)
#[1] 0

i.e. it is working fine until

df %>% 
   group_by(group) %>% 
   dplyr::filter(if(n() > 1) {(RFR_Score < Upper_SD_Threshold) } else TRUE) %>%     
   dplyr::filter(dplyr::between(RFR_Score, AvgScore_Per_Group, Upper_SD_Threshold)) %>%
   slice_max(direct_PPI_count, n = 1) %>% 
   slice_max(secondary_PPI_count, n = 1) 
# A tibble: 1 x 7
# Groups:   group [1]
#  group gene  RFR_Score AvgScore_Per_Group Upper_SD_Threshold direct_PPI_count secondary_PPI_count
#  <int> <chr>     <dbl>              <dbl>              <dbl>            <int>               <int>
#1     1 gene3       0.7               0.43               0.75                1                  45

Also, the specific error in OP's code is related to left and right of between which takes a value of length 1. If there are more than one element, it throws the length error. To circumvent, we can use first

df %>% 
 group_by(group) %>% 
 dplyr::filter(if(n() > 1) {(RFR_Score < Upper_SD_Threshold) } else TRUE) %>%
 dplyr::filter(dplyr::between(RFR_Score, first(AvgScore_Per_Group), first(Upper_SD_Threshold)) )

Upvotes: 2

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