unexpect results from p.adjust?

Question

[star]

I like to adjust my p-value results, but when I use p.adjust() function I get unexpected results as below:

df$HW_pval.adj <- p.adjust(df$HW_pval, method = "BH")

input: df

       SNP                      HW_pval         
1 10 112046150    1.37831825318596e-49           
2  10 12292454     5.11437528649252e-39           
3  10 73576307     0.747604763130749                
4  10 73994765    3.16878102556126e-31           
5  10 75881676    2.08828540782082e-40          
6  10 91066769    1.16740014071809e-34

output:

df

  SNP                     HW_pval           HW_pval.adj
1 10 112046150    1.37831825318596e-49           1
2  10 12292454     5.11437528649252e-39          1
3  10 73576307     0.747604763130749             1
4  10 73994765    3.16878102556126e-31           1
5  10 75881676    2.08828540782082e-40           1
6  10 91066769    1.16740014071809e-34           1

[Nicolas Rosewick]

could you do is(df$HW_pval) ?

[star]

is(df$HW_pval) [1] "factor" "integer" "oldClass" "numeric" "vector"

[Devon Ryan]

There's your problem. That column is being seen as a factor rather than a float with df$HW_pval <- as.numeric(as.character(df$HW_pval)).

[Giovanni M Dall'Olio]

this answer is correct. Moreover, it would be good to check the reason why the column is a factor instead of a numeric. Maybe some of the rows contain characters or invalid data for that column, causing R to think it is a character column. It would be better to track down the error and fix it.

[Devon Ryan]

What does hist(df$HW_pval) look like?