1  Sample Information

Below shows the full sample information:

library(DT)
dt.samples<-fread("static/R/data/dt.samples.csv")
dt.samples %>% DT::datatable(extensions = 'Buttons',options = list(dom="Bfrtip", buttons = c('copy', 'csv', 'excel')))

Table 1.1: Sample used in this study

Pleae note that:

• GS-B-374-UW is data from the same plasma sample as GS-B-374-UW-b. Both failed QC
• GS-59-CX is data from the same plasma sample as GS-59-CX-b. Both failed QC
• GS-179-HQ is data from the same plasma sample as GS-179-HQ-b. Only GS-179-HQ-b passed QC

Now, update the dt.samples by dropping those samples failed in QC:

Listing 1.1: Update the sample data.table

dt.samples<-dt.samples[!SampleID %in% c("GS-B-374-UW","GS-B-374-UW-b","GS-59-CX","GS-59-CX-b","GS-179-HQ")]

1.1 Discovery Cohort (preterm dataset)

Listing 1.2: Tabulate the discovery dataset

xtabs(~GA+Condition, dt.samples[Cohort=="preterm"]) %>% addmargins

      Condition
GA     Case Control Sum
  12wk   15      60  75
  20wk   14      60  74
  28wk   12      60  72
  36wk    1      54  55
  Sum    42     234 276

1.2 Validation Cohort (term dataset)

Listing 1.3: Tabulate the validation dataset

xtabs(~GA+Condition, dt.samples[Cohort=="term"]) %>% addmargins

      Condition
GA     Case Control Sum
  12wk   24      96 120
  20wk   22      96 118
  28wk   24      95 119
  36wk   21      96 117
  Sum    91     383 474