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

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 ...
differentially-expressed-genes scrna r
• 1,950 views • link
updated by Ram Ram • written by Bioinfo • Bioinfo

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

• 0 views • link
written by Nicolas Rosewick Nicolas Rosewick

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.

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written by Bioinfo • Bioinfo

1 answer

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)
• 0 views • link
updated by Ram Ram • written by Matthias Zepper Matthias Zepper

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

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written by Bioinfo • Bioinfo

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