Assess features using the quality metrics defined in (Broadhurst
2018). The quality metrics are described in Details section of
flag_quality
Usage
assess_quality(object, ...)
# S4 method for class 'MetaboSet'
assess_quality(object)
# S4 method for class 'SummarizedExperiment'
assess_quality(object, assay.type = NULL)Arguments
- object
a
SummarizedExperimentorMetaboSetobject- ...
additional arguments passed to methods
- assay.type
character, assay to be used in case of multiple assays
Examples
data(example_set)
ex_set <- assess_quality(example_set)
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 NA 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 NA 0.366231 0.383584 0.875327 1.089626
#> HILIC_neg_401_52a4_211 NA 0.153478 0.222952 0.419890 0.710290
#> ... ... ... ... ... ...
#> RP_pos_226_7218a3_1371 NA 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 NA 0.729257 0.948402 1.106946 1.207068
#> RP_pos_453_282a5_128 NA 0.663424 1.133718 1.465057 2.228991
#> RP_pos_153_9636a7_9986 NA 0.570564 0.183891 1.075597 0.439143