I have a number of large datasets with ~10 columns, and ~200000 rows. Not all columns contain values for each row, although at least one column must contain a value for the row to be present, I would like to set a threshold for how many NA
s are allowed in a row.
My Dataframe looks something like this:
ID q r s t u v w x y z
A 1 5 NA 3 8 9 NA 8 6 4
B 5 NA 4 6 1 9 7 4 9 3
C NA 9 4 NA 4 8 4 NA 5 NA
D 2 2 6 8 4 NA 3 7 1 32
And I would like to be able to delete the rows that contain more than 2 cells containing NA to get
ID q r s t u v w x y z
A 1 5 NA 3 8 9 NA 8 6 4
B 5 NA 4 6 1 9 7 4 9 3
D 2 2 6 8 4 NA 3 7 1 32
complete.cases
removes all rows containing any NA
, and I know one can delete rows that contain NA
in certain columns but is there a way to modify it so that it is non-specific about which columns contain NA
, but how many of the total do?
Alternatively, this dataframe is generated by merging several dataframes using
file1<-read.delim("~/file1.txt")
file2<-read.delim(file=args[1])
file1<-merge(file1,file2,by="chr.pos",all=TRUE)
Perhaps the merge function could be altered?
Thanks
Use rowSums
. To remove rows from a data frame (df
) that contain precisely n NA
values:
df <- df[rowSums(is.na(df)) != n, ]
or to remove rows that contain n or more NA
values:
df <- df[rowSums(is.na(df)) < n, ]
in both cases of course replacing n
with the number that's required
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