pfilter.gds {bigmelon} | R Documentation |
The pfilter function filters data sets based on bead count and
detection p-values. The user can set their own thresholds or use
the default pfilter settings. This specific function will take a Genomic Data
Structure (GDS) file as input and perform pfilter similar to how
pfilter
in wateRmelon is performed.
## S4 method for signature 'gds.class' pfilter(mn, perCount = NULL, pnthresh = NULL, perc = NULL, pthresh = NULL)
mn |
a gds object OR node corresponding to methylated intensities |
perCount |
remove sites having this percentage of samples with a beadcount <3, default = 5 |
pnthresh |
cut off for detection p-value, default= 0.05 |
perc |
remove sample having this percentage of sites with a detection p-value greater than pnthresh, default = 1 |
pthresh |
remove sites having this percentage of sample with a detection p-value greater than pnthresh, default = 1 |
See pfilter
. If using pfilter.gds, function
will return a list of two elements. Both logical vectors with length(nrow) and length(ncol), which can be used for subsetting. Otherwise will be used to subset data directly.
Tyler Gorrie-Stone, Original (wateRmelon) Function by Ruth Pidsley
data(melon) e <- es2gds(melon, "melon.gds") pfilter(e) closefn.gds(e) unlink("melon.gds")