Error in as.peakData with NA's and check_rows = T

[clabornd]

The below fails

library(ftmsRanalysis)
data("ftms12T_edata")
data("ftms12T_fdata")
data("ftms12T_emeta")

edata <- ftms12T_edata
edata[edata == 0] <- NA
peakObj <- as.peakData(edata, ftms12T_fdata, ftms12T_emeta, 
                       edata_cname="Mass", fdata_cname="SampleID", 
                       mass_cname="Mass", c_cname="C", h_cname="H", 
                       o_cname="O", n_cname="N", s_cname="S", 
                       p_cname="P", isotopic_cname = "C13", 
                       isotopic_notation = "1", check_rows = T)

Error in if (any(molfilt$Num_Observations == 0)) res <- applyFilt(molfilt,  : 
  missing value where TRUE/FALSE needed

The error appears to begin with the molecule_filter() call:

ftmsRanalysis/R/as.ftmsData.R

Line 291 in 13634ad

molfilt <- molecule_filter(res)

which then calls n_present(), which calls rowSums() on an object with NA's producing NA's in the output:

ftmsRanalysis/R/group_summary_functions.R

Line 12 in 13634ad

res <- as.integer(rowSums(x>0))

Then the any() call in the error message returns an NA since molfilt$Num_Observations contains NA's.

[clabornd]

fixed by #12