Flags features with too high amount of missing values. There are two
detection rate limits, both defined as the minimum proportion of samples
that need to have a value (not NA) for the feature to be kept.
'qc_limit is the detection rate limit for QC samples,
'group_limit is the detection rate limit for the actual study groups.
If the group limit is passed for AT LEAST ONE GROUP, then the feature is
kept. Features with low detection rate in QCs are flagged as
"Low_qc_detection", while low detection rate in the study groups is flagged
as "Low_group_detection". The detection rates for all the groups are
recorded in feature data.
Arguments
- object
a
SummarizedExperimentorMetaboSetobject- qc_limit
the detection rate limit for QC samples
- group_limit
the detection rate limit for study groups
- group
the columns name in sample information to use as the grouping variable
- assay.type
character, assay to be used in case of multiple assays
Examples
data(example_set)
ex_set <- mark_nas(example_set, value = 0)
ex_set <- flag_detection(ex_set, group = "Group")
#> INFO [2025-06-23 22:36:34]
#> 1% of features flagged for low detection rate
rowData(ex_set)
#> DataFrame with 80 rows and 11 columns
#> Feature_ID Split Alignment
#> <character> <character> <integer>
#> HILIC_neg_259_9623a4_4322 HILIC_neg_259_9623a4.. HILIC_neg 1
#> HILIC_neg_108_1065a2_6121 HILIC_neg_108_1065a2.. HILIC_neg 2
#> HILIC_neg_158_23a1_4128 HILIC_neg_158_23a1_4.. HILIC_neg 3
#> HILIC_neg_251_0056a0_6161 HILIC_neg_251_0056a0.. HILIC_neg 4
#> HILIC_neg_401_52a4_211 HILIC_neg_401_52a4_211 HILIC_neg 5
#> ... ... ... ...
#> RP_pos_226_7218a3_1371 RP_pos_226_7218a3_1371 RP_pos 16
#> RP_pos_280_3779a4_0424 RP_pos_280_3779a4_0424 RP_pos 17
#> RP_pos_447_3232a2_2393 RP_pos_447_3232a2_2393 RP_pos 18
#> RP_pos_453_282a5_128 RP_pos_453_282a5_128 RP_pos 19
#> RP_pos_153_9636a7_9986 RP_pos_153_9636a7_9986 RP_pos 20
#> Average_Mz Average_Rt_min Column Ion_mode
#> <numeric> <numeric> <character> <character>
#> HILIC_neg_259_9623a4_4322 259.962 4.432241 HILIC neg
#> HILIC_neg_108_1065a2_6121 108.107 2.612073 HILIC neg
#> HILIC_neg_158_23a1_4128 158.230 1.412822 HILIC neg
#> HILIC_neg_251_0056a0_6161 251.006 0.616145 HILIC neg
#> HILIC_neg_401_52a4_211 401.520 4.210970 HILIC neg
#> ... ... ... ... ...
#> RP_pos_226_7218a3_1371 226.722 3.13714 RP pos
#> RP_pos_280_3779a4_0424 280.378 4.04238 RP pos
#> RP_pos_447_3232a2_2393 447.323 2.23926 RP pos
#> RP_pos_453_282a5_128 453.282 5.12797 RP pos
#> RP_pos_153_9636a7_9986 153.964 7.99864 RP pos
#> Flag Detection_rate_Group_A
#> <character> <numeric>
#> HILIC_neg_259_9623a4_4322 NA 0.95
#> HILIC_neg_108_1065a2_6121 NA 0.90
#> HILIC_neg_158_23a1_4128 NA 0.95
#> HILIC_neg_251_0056a0_6161 NA 0.90
#> HILIC_neg_401_52a4_211 NA 0.95
#> ... ... ...
#> RP_pos_226_7218a3_1371 NA 0.85
#> RP_pos_280_3779a4_0424 NA 0.85
#> RP_pos_447_3232a2_2393 NA 0.95
#> RP_pos_453_282a5_128 NA 0.90
#> RP_pos_153_9636a7_9986 NA 0.80
#> Detection_rate_Group_B Detection_rate_QC
#> <numeric> <numeric>
#> HILIC_neg_259_9623a4_4322 0.90 1.0
#> HILIC_neg_108_1065a2_6121 0.95 0.9
#> HILIC_neg_158_23a1_4128 0.90 0.8
#> HILIC_neg_251_0056a0_6161 0.95 1.0
#> HILIC_neg_401_52a4_211 0.95 1.0
#> ... ... ...
#> RP_pos_226_7218a3_1371 0.9 0.9
#> RP_pos_280_3779a4_0424 0.9 1.0
#> RP_pos_447_3232a2_2393 0.9 0.9
#> RP_pos_453_282a5_128 1.0 0.8
#> RP_pos_153_9636a7_9986 0.9 0.8