Flags low-quality features using the quality metrics defined in (Broadhurst
2018). The metrics are described in more detain in Details. A condition for
keeping the features is given as a character, which is passed to
filter.
Usage
flag_quality
flag_quality(object, assay.type = NULL, condition =
"(RSD_r < 0.2 & D_ratio_r < 0.4) |
(RSD < 0.1 & RSD_r < 0.1 & D_ratio < 0.1)")Arguments
- object
a
SummarizedExperimentorMetaboSetobject- assay.type
character, assay to be used in case of multiple assays
- condition
character, condition for keeping the features, see Details
Details
The quality metrics measure two things: internal spread of the QCs, and spread of the QCs compared to the spread of the biological samples. Internal spread is measured with relative standard deviation (RSD), also known as coefficient of variation (CV). $$RSD = sd(QC) / mean(QC) $$ Where \(sd(QC)\) is the standard deviation of the QC samples and '\(mean(QC)\) is the sample mean of the signal in the QC samples. RSD can also be replaced by a non-parametric, robust version based on the median and median absolute deviation (MAD): $$RSD_r = 1.4826 * MAD(QC) / median(QC)$$ The spread of the QC samples compared to the biological samples is measured using a metric called D-ratio: $$D_ratio = sd(QC) / sd(biological)$$ Or, as before, a non-parametric, robust alternative: $$D_ratio_r = MAD(QC) / MAD(biolofical) $$ The default condition keeps features that pass either of the two following conditions: $$RSD_r < 0.2 \& D_ratio_r < 0.4$$ $$RSD < 0.1 \& RSD_r < 0.1 \& D_ratio < 0.1$$
References
Broadhurst, David et al. Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies. Metabolomics : Official journal of the Metabolomic Society vol. 14,6 (2018): 72. doi:10.1007/s11306-018-1367-3
Examples
data(example_set)
ex_set <- flag_quality(example_set)
#> INFO [2025-06-23 22:36:34]
#> 92% of features flagged for low quality
rowData(ex_set)
#> DataFrame with 80 rows and 12 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 RSD RSD_r D_ratio D_ratio_r
#> <character> <numeric> <numeric> <numeric> <numeric>
#> HILIC_neg_259_9623a4_4322 Low_quality 0.127075 0.156465 0.363022 0.475271
#> HILIC_neg_108_1065a2_6121 Low_quality 0.468943 0.375347 1.202952 1.223426
#> HILIC_neg_158_23a1_4128 Low_quality 0.568911 0.188623 1.019238 0.509172
#> HILIC_neg_251_0056a0_6161 Low_quality 0.366231 0.383584 0.875327 1.089626
#> HILIC_neg_401_52a4_211 Low_quality 0.153478 0.222952 0.419890 0.710290
#> ... ... ... ... ... ...
#> RP_pos_226_7218a3_1371 Low_quality 0.419258 0.298690 0.986842 1.069176
#> RP_pos_280_3779a4_0424 NA 0.126026 0.173915 0.253066 0.370787
#> RP_pos_447_3232a2_2393 Low_quality 0.729257 0.948402 1.106946 1.207068
#> RP_pos_453_282a5_128 Low_quality 0.663424 1.133718 1.465057 2.228991
#> RP_pos_153_9636a7_9986 Low_quality 0.570564 0.183891 1.075597 0.439143
# Custom condition
ex_set <- flag_quality(example_set,
condition = "RSD_r < 0.3 & D_ratio_r < 0.6")
#> INFO [2025-06-23 22:36:35]
#> 70% of features flagged for low quality
rowData(ex_set)
#> DataFrame with 80 rows and 12 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 RSD RSD_r D_ratio D_ratio_r
#> <character> <numeric> <numeric> <numeric> <numeric>
#> HILIC_neg_259_9623a4_4322 NA 0.127075 0.156465 0.363022 0.475271
#> HILIC_neg_108_1065a2_6121 Low_quality 0.468943 0.375347 1.202952 1.223426
#> HILIC_neg_158_23a1_4128 NA 0.568911 0.188623 1.019238 0.509172
#> HILIC_neg_251_0056a0_6161 Low_quality 0.366231 0.383584 0.875327 1.089626
#> HILIC_neg_401_52a4_211 Low_quality 0.153478 0.222952 0.419890 0.710290
#> ... ... ... ... ... ...
#> RP_pos_226_7218a3_1371 Low_quality 0.419258 0.298690 0.986842 1.069176
#> RP_pos_280_3779a4_0424 NA 0.126026 0.173915 0.253066 0.370787
#> RP_pos_447_3232a2_2393 Low_quality 0.729257 0.948402 1.106946 1.207068
#> RP_pos_453_282a5_128 Low_quality 0.663424 1.133718 1.465057 2.228991
#> RP_pos_153_9636a7_9986 NA 0.570564 0.183891 1.075597 0.439143