How can we separate downregulated genes and upregulated genes from list of dataframes separately??

Question

[Bioinfo]

This is the list of dataframes from which i need to separate out UP and down regulated genes in a form of dataframes only means two separate list of genes(up and down) with dataframes.

str(FindMarkers_list)

    List of 4
     $ 0 :'data.frame': 1730 obs. of  5 variables:
      ..$ p_val     : num [1:1730] 7.02e-154 1.04e-116 4.45e-86 1.52e-82 2.32e-78 ...
      ..$ avg_log2FC: num [1:1730] 1.341 1.015 3.719 1.329 0.679 ...
      ..$ pct.1     : num [1:1730] 0.631 0.468 0.83 0.66 0.234 0.617 0.688 0.73 0.56 0.319 ...
      ..$ pct.2     : num [1:1730] 0.04 0.027 0.228 0.119 0.007 0.99 0.149 0.172 0.092 0.022 ...
      ..$ p_val_adj : num [1:1730] 1.61e-149 2.39e-112 1.02e-81 3.48e-78 5.31e-74 ...
     $ 1 :'data.frame': 1755 obs. of  5 variables:
      ..$ p_val     : num [1:1755] 4.14e-240 2.34e-120 1.87e-116 1.50e-87 2.69e-85 ...
      ..$ avg_log2FC: num [1:1755] -2.52 -2.75 -1.89 -1.2 -1.11 ...
      ..$ pct.1     : num [1:1755] 0 0.19 0.12 0.038 0 0.397 0.007 0.072 0.118 0.386 ...
      ..$ pct.2     : num [1:1755] 0.687 0.806 0.757 0.448 0.257 0.881 0.287 0.526 0.631 0.866 ...
      ..$ p_val_adj : num [1:1755] 9.47e-236 5.36e-116 4.28e-112 3.43e-83 6.16e-81 ...
 $ 2 :'data.frame': 1828 obs. of  5 variables:
  ..$ p_val     : num [1:1828] 4.13e-191 3.41e-147 4.16e-142 1.80e-141 7.22e-136 ...
  ..$ avg_log2FC: num [1:1828] -3.14 -2.07 -2.01 -1.74 -2.07 ...
  ..$ pct.1     : num [1:1828] 0 0.52 0.913 0.778 0.111 0.997 0.951 0.28 0.459 0.331 ...
  ..$ pct.2     : num [1:1828] 0.925 0.998 0.998 0.993 0.89 1 1 0.965 0.983 0.94 ...
  ..$ p_val_adj : num [1:1828] 9.45e-187 7.81e-143 9.52e-138 4.11e-137 1.65e-131 ...
 $ 3 :'data.frame': 2959 obs. of  5 variables:
  ..$ p_val     : num [1:2959] 2.44e-70 6.15e-49 2.02e-43 7.23e-42 2.83e-37 ...
  ..$ avg_log2FC: num [1:2959] -1.45 -1.38 -2.32 -3.62 -1.84 ...
  ..$ pct.1     : num [1:2959] 0 0.021 0 0.006 0.104 0.138 0 0 0.972 0.061 ...
  ..$ pct.2     : num [1:2959] 0.433 0.483 0.267 0.317 0.7 0.783 0.217 0.217 0.25 0.55 ...
  ..$ p_val_adj : num [1:2959] 5.58e-66 1.41e-44 4.63e-39 1.66e-37 6.47e-33 ...

[Nicolas Rosewick]

not sure what you want but if you need to translate your list of two dataframes within one dataframe you can use do.call(rbind,dat) if dat is your list input list

[Bioinfo]

Thanks Nicolas for the response

I want to separate above mentioned list into two separate list with same format dataframes. Genes names are present in each rows. list 1 i.e. up_regulated_genes <- avg_log2FC > 0 & p_val < 0.05 list 2 i.e. down_regulated_genes <- avg_log2FC < 0 & p_val > 0.05

Thanks in advance.

Answer 1

[Matthias Zepper]

With lapply(), you can apply any function to each list element:

up_regulated_genes <- lapply(FindMarkers_list, subset, avg_log2FC > 0, p_val < 0.05)
down_regulated_genes <- lapply(FindMarkers_list, subset, avg_log2FC < 0, p_val < 0.05)

[Bioinfo]

Thank you so much... it works. Thanks a lot.