How can we separate downregulated genes and upregulated genes from list of dataframes separately??
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Entering edit mode
14 months ago
Bioinfo ▴ 30

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 • 887 views
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Entering edit mode

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

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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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2
Entering edit mode
14 months ago

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

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