Return the IDs of flagged samples for objects of the outlier_map
or
missingness_map
classes. Samples are flagged based on the percent
analytes (RFU columns) for a given sample that were identified as outliers using
the median absolute deviation (MAD), or the percent of "missingness" (NAs
) of
clinical meta data of an ADAT.
Arguments
- x
An object of class:
outlier_map
- fromcalcOutlierMap()
missingness_map
- fromcalcMissingnessMap()
- flags
Numeric in
[0, 1]
. For an"outlier_map"
, the proportion of the analytes (columns) for a given sample that must be outliers for a flag to be placed at the right-axis, thus flagging that sample. For"missingness_map"
class, the percent of "missingness" (NAs
) of the clinical meta data. IfNULL
(default),0.05
(5%) is selected.- data
Optional. The data originally used to create the map
x
. If omitted, a single column data frame is returned.- include
Optional. Character vector of column name(s) in
data
to include in the resulting data frame. Ignored ifdata = NULL
.
Value
A data.frame
of the indices (idx
) of flagged samples, along
with any additional variables as specified by include
.
See also
Other Calc Map:
calcFoldchangeMatrix()
,
calcMissingnessMap()
,
calcOutlierMap()
,
plot.Map()
Examples
# flagged outliers
# create a single sample outlier (12)
out_adat <- SomaDataIO::example_data
apts <- SomaDataIO::getAnalytes(out_adat)
out_adat[12, apts] <- out_adat[12, apts] * 10
om <- calcOutlierMap(out_adat)
getFlaggedIds(om, out_adat, flags = 0.05, include = c("Sex", "Subarray"))
#> idx Sex Subarray
#> 1 12 M 5
#> 2 13 <NA> 4
#> 3 43 <NA> 8
#> 4 87 <NA> 6
#> 5 143 <NA> 4
#> 6 151 <NA> 4
#> 7 173 <NA> 4
# flagged missingness
sample.adat <- SomaDataIO::example_data
nc <- SomaDataIO::getMeta(sample.adat, n = TRUE)
meta <- sample.adat[, SomaDataIO::getMeta(sample.adat)]
# random assign NAs to df b/c currently none missing
cols <- rep(1:nc, each = 3L)
rows <- withr::with_seed(1, as.integer(replicate(nc, sample(1:nrow(meta), 3))))
meta[cbind(rows, cols)] <- NA
mm <- calcMissingnessMap(meta)
getFlaggedIds(mm, meta, flags = 0.2)
#> idx
#> 1 1
#> 2 2
#> 3 3
#> 4 4
#> 5 5
#> 6 6
#> 7 7
#> 8 8
#> 9 9
#> 10 10
#> 11 11
#> 12 12
#> 13 13
#> 14 14
#> 15 15
#> 16 16
#> 17 17
#> 18 18
#> 19 19
#> 20 20
#> 21 21
#> 22 22
#> 23 23
#> 24 24
#> 25 25
#> 26 26
#> 27 27
#> 28 28
#> 29 29
#> 30 30
#> 31 31
#> 32 32
#> 33 33
#> 34 34
#> 35 35
#> 36 36
#> 37 37
#> 38 38
#> 39 39
#> 40 40
#> 41 41
#> 42 42
#> 43 43
#> 44 44
#> 45 45
#> 46 46
#> 47 47
#> 48 48
#> 49 49
#> 50 50
#> 51 51
#> 52 52
#> 53 53
#> 54 54
#> 55 55
#> 56 56
#> 57 57
#> 58 58
#> 59 59
#> 60 60
#> 61 61
#> 62 62
#> 63 63
#> 64 64
#> 65 65
#> 66 66
#> 67 67
#> 68 68
#> 69 69
#> 70 70
#> 71 71
#> 72 72
#> 73 73
#> 74 74
#> 75 75
#> 76 76
#> 77 77
#> 78 78
#> 79 79
#> 80 80
#> 81 81
#> 82 82
#> 83 83
#> 84 84
#> 85 85
#> 86 86
#> 87 87
#> 88 88
#> 89 89
#> 90 90
#> 91 91
#> 92 92
#> 93 93
#> 94 94
#> 95 95
#> 96 96
#> 97 97
#> 98 98
#> 99 99
#> 100 100
#> 101 101
#> 102 102
#> 103 103
#> 104 104
#> 105 105
#> 106 106
#> 107 107
#> 108 108
#> 109 109
#> 110 110
#> 111 111
#> 112 112
#> 113 113
#> 114 114
#> 115 115
#> 116 116
#> 117 117
#> 118 118
#> 119 119
#> 120 120
#> 121 121
#> 122 122
#> 123 123
#> 124 124
#> 125 125
#> 126 126
#> 127 127
#> 128 128
#> 129 129
#> 130 130
#> 131 131
#> 132 132
#> 133 133
#> 134 134
#> 135 135
#> 136 136
#> 137 137
#> 138 138
#> 139 139
#> 140 140
#> 141 141
#> 142 142
#> 143 143
#> 144 144
#> 145 145
#> 146 146
#> 147 147
#> 148 148
#> 149 149
#> 150 150
#> 151 151
#> 152 152
#> 153 153
#> 154 154
#> 155 155
#> 156 156
#> 157 157
#> 158 158
#> 159 159
#> 160 160
#> 161 161
#> 162 162
#> 163 163
#> 164 164
#> 165 165
#> 166 166
#> 167 167
#> 168 168
#> 169 169
#> 170 170
#> 171 171
#> 172 172
#> 173 173
#> 174 174
#> 175 175
#> 176 176
#> 177 177
#> 178 178
#> 179 179
#> 180 180
#> 181 181
#> 182 182
#> 183 183
#> 184 184
#> 185 185
#> 186 186
#> 187 187
#> 188 188
#> 189 189
#> 190 190
#> 191 191
#> 192 192