forked from molgenis/ngs-utils
-
Notifications
You must be signed in to change notification settings - Fork 0
/
NIPT_Diagnostics_v3.0_Report.Rmd
117 lines (86 loc) · 4.9 KB
/
NIPT_Diagnostics_v3.0_Report.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
Uitslag `r samplename`
=======================================================
`r format(Sys.Date(), format=("%d %B %Y"))`
### Chromosome 13
```{r echo=FALSE, results='asis'}
library(xtable)
#Build list from variables
Variation_coefficient <- c(format(CV13_1, digits = 2),
format(CV13_2, digits = 2),
format(CV13_3, digits = 2),
format(CV13_4,digits = 2) )
Normal_Distribution <- c(format(Normal13_1),
format(Normal13_2),
format(Normal13_3),
format(Normal13_4) )
Z_score <- c(format(round(Zscore13_1,2), digits = 3, nsmall = 2),
format(round(Zscore13_2,2), digits = 3, nsmall = 2),
format(round(Zscore13_3,2), digits = 3, nsmall = 2),
format(round(Zscore13_4,2), digits = 3, nsmall = 2) )
Posterior_risk <- c(format(round(posteriorrisk13_1,1), digits = 3, nsmall = 1),
format(round(posteriorrisk13_2,1), digits = 3, nsmall = 1),
format(round(posteriorrisk13_3,1), digits = 3, nsmall = 1),
format(round(posteriorrisk13_4,1), digits = 3, nsmall = 1) )
Median_PR <- c(format(round(medianposteriorrisk13,1), digits = 3, nsmall = 1),"","","")
apriori <- c(format(apriori13),"","","")
datafr13=data.frame(Variation_coefficient,Normal_Distribution,Z_score,Posterior_risk,Median_PR,apriori, row.names = c("1","2","3","4"))
#Transform to table
tab <- xtable(datafr13, align = "ccccccc")
print(tab, type="html")
#tab <- xtable(list13)
#print(tab, type="html")
```
### Chromosome 18
```{r echo=FALSE, results='asis'}
library(xtable)
#Build list from variables
Variation_coefficient <- c(format(CV18_1, digits = 2),
format(CV18_2, digits = 2),
format(CV18_3, digits = 2),
format(CV18_4,digits = 2) )
Normal_Distribution <- c(format(Normal18_1),
format(Normal18_2),
format(Normal18_3),
format(Normal18_4) )
Z_score <- c(format(round(Zscore18_1,2), digits = 3, nsmall = 2),
format(round(Zscore18_2,2), digits = 3, nsmall = 2),
format(round(Zscore18_3,2), digits = 3, nsmall = 2),
format(round(Zscore18_4,2), digits = 3, nsmall = 2) )
Posterior_risk <- c(format(round(posteriorrisk18_1,1), digits = 3, nsmall = 1),
format(round(posteriorrisk18_2,1), digits = 3, nsmall = 1),
format(round(posteriorrisk18_3,1), digits = 3, nsmall = 1),
format(round(posteriorrisk18_4,1), digits = 3, nsmall = 1) )
Median_PR <- c(format(round(medianposteriorrisk18,1), digits = 3, nsmall = 1),"","","")
apriori <- c(format(apriori18),"","","")
datafr18=data.frame(Variation_coefficient ,Normal_Distribution,Z_score,Posterior_risk,Median_PR,apriori, row.names = c("1","2","3","4"))
#Transform to table
tab <- xtable(datafr18, align = "ccccccc")
print(tab, type="html")
```
### Chromosome 21
```{r echo=FALSE, results='asis'}
library(xtable)
#Build list from variables
Variation_coefficient <- c(format(CV21_1, digits = 2),
format(CV21_2, digits = 2),
format(CV21_3, digits = 2),
format(CV21_4,digits = 2) )
Normal_Distribution <- c(format(Normal21_1),
format(Normal21_2),
format(Normal21_3),
format(Normal21_4) )
Z_score <- c(format(round(Zscore21_1,2), digits = 3, nsmall = 2),
format(round(Zscore21_2,2), digits = 3, nsmall = 2),
format(round(Zscore21_3,2), digits = 3, nsmall = 2),
format(round(Zscore21_4,2), digits = 3, nsmall = 2) )
Posterior_risk <- c(format(round(posteriorrisk21_1,1), digits = 3, nsmall = 1),
format(round(posteriorrisk21_2,1), digits = 3, nsmall = 1),
format(round(posteriorrisk21_3,1), digits = 3, nsmall = 1),
format(round(posteriorrisk21_4,1), digits = 3, nsmall = 1) )
Median_PR <- c(format(round(medianposteriorrisk21,1), digits = 3, nsmall = 1),"","","")
apriori <- c(format(apriori21),"","","")
datafr21=data.frame(Variation_coefficient ,Normal_Distribution,Z_score,Posterior_risk,Median_PR,apriori, row.names = c("1","2","3","4"))
#Transform to table
tab <- xtable(datafr21, align = "ccccccc")
print(tab, type="html")
```