Using grep to filter rows between two files

Question

I have one file tab and one file lrt$fitted.values . I would like to take the IDs GeneID from tab and filter out the rows in lrt$fitted.values that matches this GeneID

I tried something like this:

grep(tab$GeneID,lrt$fitted.values)

my files:

tab
                                               GeneID     logFC  logCPM       LR       PValue        FDR
hsa-miR-20b-5p|hsa-mir-20b hsa-miR-20b-5p|hsa-mir-20b -1.802771 5.28974 14.69575 0.0001263309 0.02728747


head(lrt$fitted.values)
                                124G      356G      126G      235G       46G      243G       82G       68G       192G
hsa-let-7a-5p|hsa-let-7a-1 32183.896 29310.569 69804.995 66689.788 59921.623 64198.314 31899.265 59945.275 56539.4487
hsa-let-7a-5p|hsa-let-7a-2 32180.380 29307.367 69797.369 66682.502 59915.077 64186.624 31895.780 59934.359 56529.1532
hsa-let-7a-5p|hsa-let-7a-3 32103.732 29237.562 69631.124 66523.676 59772.369 64016.191 31819.810 59775.218 56379.0534
hsa-let-7b-5p|hsa-let-7b   12255.487 11161.337 26581.438 25395.180 22817.893 23257.116 12147.101 21716.368 20482.5400
hsa-let-7c-5p|hsa-let-7c    1120.679  1020.626  2430.686  2322.211  2086.537  1105.720  1110.767  1032.467   973.8072
hsa-let-7d-5p|hsa-let-7d    2955.159  2691.327  6409.567  6123.525  5502.065  5455.887  2929.024  5094.443  4804.9994

Answer 1

I am assuming your files are loaded into R as dataframes (based on the $ ). If you want to filter the lrt$fitted.values dataframe based on a list of exclusion values I would do something like this:

 #list of exclusion values
 negvalues <- tab$GeneID

 # exclude those values based on rownames.
 df    <- lrt$fitted.values
 df[!rownames(df) %in% negvalues,]

%in% will check for membership in the list; ! will negate the lookup.