r - Check a partial dataframe of p-values above 1 if so than set to 1 -

i have following table:

myfamdf <- structure(list(x = c("ets", "fh", "hlh", "hmg", "homeo", "homeo ",  "homeo, pou", "irf", "unknown", "zn2cys6", "znf_c2h2", "znf_c4" ), mashvstrap = c(7.57756175712832e-05, 2.16501764489381e-05,  1.28838720843028e-05, 7.61948145586808e-26, 2.60621688448055e-53,  5.65846675050138e-11, 2.8351421540276e-06, 2.16501764489381e-05,  3.2934292268274e-24, 2.82352692734938e-05, 6.64390583188061e-16,  1.0825088224469e-05), mashvsbeeml = c(0.000205676676264912, 0.00519604234774513,  0.00724381285695056, 0.864846903741683, 5.63594927321681e-06,  0.212004750633662, 0.519032309279987, 0.0114962436943861, 0.0364539615325715,  0.00226912148014415, 0.00150554384087195, 0.165493948775683),      trapvsbeeml = c(1.0825088224469e-05, 1.0825088224469e-05,      5.2304674730304e-05, 3.24328889627148e-13, 8.6852178695266e-46,      7.60650709869649e-06, 2.8351421540276e-06, 1.0825088224469e-05,      1.35923430631341e-18, 1.03873566123765e-06, 4.36897483629527e-17,      1.0825088224469e-05), frequency = c(10l, 10l, 13l, 44l, 158l,      19l, 11l, 10l, 121l, 17l, 54l, 10l), mash_mean = c(0.524697080582274,      0.533031100926345, 0.612272921172441, 0.554248028314286,      0.718880708100701, 0.669975051155167, 0.689738366117961,      0.523671096430599, 0.441776560865089, 0.379363597547222,      0.549419213423343, 0.662304821003215), beeml_mean = c(0.666798180226875,      0.660863667642578, 0.744265111335818, 0.475324697683268,      0.730669935762911, 0.650768612120795, 0.704779617351813,      0.623826799121585, 0.487316361691942, 0.608017794324143,      0.637626824316619, 0.732392229673044), trap_mean = c(0.297319284507052,      0.270211650098443, 0.261921495552034, 0.124938264266261,      0.171602908725421, 0.138827064266711, 0.180368231533709,      0.279573714498502, 0.162194901674355, 0.127782526341284,      0.249250520527459, 0.274929655041024)), .names = c("x", "mashvstrap",  "mashvsbeeml", "trapvsbeeml", "frequency", "mash_mean", "beeml_mean",  "trap_mean"), class = "data.frame", row.names = c(na, -12l)) 

now have problem after multiple test correction there exist p-values above 1, , should set 1 again. thought easy sapply gives me error

error in matrix(unlist(value, recursive = false, use.names = false), nrow = nr, : 'data' must of vector type, 'null

my try was:

myfamdf[, 2:4] <- sapply(myfamdf[,2:4], function(x){if(myfamdf[, 2:4][x] >= 1) {myfamdf[, 2:4] = 1}})

what doing wrong , why sapply see list(data.frame) type null.

you don't need rereference myfamdf in function in sapply. function takes single columns argument. so, can write

myfamdf[, 2:4] <- sapply(data.frame(myfamdf[,2:4]),                  function(x) ifelse(x>1,1,x)) 

as noted @joran, data.frame not needed.

myfamdf[, 2:4] <- sapply(myfamdf[,2:4], function(x) ifelse(x>1,1,x))