vignettes/error_no_subject_qc.Rmd
error_no_subject_qc.RmdWhen you use the functions which need specific identification for
Subject or QC samples in class of
sample_info, if there is a error:
Error: error: No Subject samples in object, please check and see here:You need to change the column class in
sample_info.
library(masscleaner)
library(tidyverse)
object@sample_info$class
#> [1] "case" "case" "case" "case" "case" "case" "case"
#> [8] "case" "case" "case" "case" "case" "case" "case"
#> [15] "case" "case" "case" "case" "case" "case" "case"
#> [22] "case" "case" "case" "case" "case" "case" "case"
#> [29] "case" "case" "case" "case" "case" "case" "case"
#> [36] "case" "case" "case" "case" "case" "case" "case"
#> [43] "case" "case" "case" "case" "case" "case" "case"
#> [50] "case" "case" "case" "case" "case" "case" "case"
#> [57] "case" "case" "case" "case" "case" "case" "case"
#> [64] "case" "case" "case" "case" "case" "case" "case"
#> [71] "case" "case" "case" "case" "case" "case" "case"
#> [78] "case" "case" "case" "case" "case" "case" "case"
#> [85] "case" "case" "case" "case" "case" "case" "case"
#> [92] "case" "case" "case" "case" "case" "case" "case"
#> [99] "case" "case" "case" "case" "case" "case" "case"
#> [106] "case" "case" "case" "case" "case" "case" "case"
#> [113] "case" "case" "case" "case" "case" "case" "case"
#> [120] "case" "case" "case" "case" "case" "case" "case"
#> [127] "case" "case" "case" "case" "case" "case" "case"
#> [134] "case" "case" "case" "case" "case" "case" "case"
#> [141] "case" "case" "case" "case" "case" "case" "case"
#> [148] "case" "case" "case" "case" "case" "case" "case"
#> [155] "case" "case" "case" "case" "case" "case" "case"
#> [162] "case" "case" "case" "case" "case" "case" "case"
#> [169] "case" "case" "case" "case" "case" "case" "case"
#> [176] "case" "case" "case" "case" "case" "case" "case"
#> [183] "case" "case" "case" "case" "case" "case" "case"
#> [190] "case" "case" "case" "case" "case" "case" "case"
#> [197] "case" "case" "case" "case" "case" "case" "case"
#> [204] "case" "case" "case" "case" "case" "case" "case"
#> [211] "case" "case" "case" "case" "case" "case" "case"
#> [218] "case" "case" "case" "case" "case" "case" "case"
#> [225] "case" "case" "case" "case" "case" "control" "control"
#> [232] "control" "control" "control" "control" "control" "control" "control"
#> [239] "control" "control" "control" "control" "control" "control" "control"
#> [246] "control" "control" "control" "control" "control" "control" "control"
#> [253] "control" "control" "control" "control" "control" "control" "control"
#> [260] "control" "control" "control" "control" "control" "control" "control"
#> [267] "control" "control" "control" "control" "control" "QC" "QC"
#> [274] "QC" "QC" "QC" "QC" "QC" "QC" "QC"
#> [281] "QC" "QC" "QC" "QC" "QC" "QC" "QC"
#> [288] "QC" "QC" "QC" "QC" "QC" "QC" "QC"
#> [295] "QC" "QC" "QC" "QC" "QC"We can see there are no “Subject” in the class, so we need to change
the case and control to
Subject.
object <-
object %>%
activate_mass_dataset(what = "sample_info") %>%
mutate(class = case_when(
class == "QC" ~ "QC",
TRUE ~ "Subject"
))
object@sample_info$class
#> [1] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [8] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [15] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [22] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [29] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [36] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [43] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [50] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [57] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [64] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [71] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [78] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [85] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [92] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [99] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [106] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [113] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [120] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [127] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [134] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [141] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [148] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [155] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [162] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [169] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [176] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [183] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [190] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [197] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [204] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [211] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [218] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [225] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [232] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [239] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [246] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [253] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [260] "Subject" "Subject" "Subject" "Subject" "Subject" "Subject" "Subject"
#> [267] "Subject" "Subject" "Subject" "Subject" "Subject" "QC" "QC"
#> [274] "QC" "QC" "QC" "QC" "QC" "QC" "QC"
#> [281] "QC" "QC" "QC" "QC" "QC" "QC" "QC"
#> [288] "QC" "QC" "QC" "QC" "QC" "QC" "QC"
#> [295] "QC" "QC" "QC" "QC" "QC"
sessionInfo()
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#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur 10.16
#>
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#> locale:
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#>
#> attached base packages:
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