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29 lines
841 B
R
29 lines
841 B
R
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library(dplyr)
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example_isolates %>%
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select(mo, where(is.rsi)) %>%
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tidyr::pivot_longer(cols = where(is.rsi)) %>%
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# remove intrisic R
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filter(!paste(mo, name) %in% AMR:::INTRINSIC_R) %>%
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mutate(name = as.ab(name),
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value = ifelse(value == "R", 1, 0),
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class = ab_group(name)) %>%
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group_by(mo, class) %>%
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summarise(n = n(),
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res = mean(value, na.rm = TRUE)) %>%
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filter(n > 30, !is.na(res))
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df <- example_isolates
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search_mo <- "B_ESCHR_COLI"
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intrinsic_res <- INTRINSIC_R[INTRINSIC_R %like% search_mo]
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intrinsic_res <- gsub(".* (.*)", "\\1", intrinsic_res)
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x <- df %>%
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select(mo, where(is.rsi)) %>%
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filter(mo == search_mo) %>%
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# at least 30 results available
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select(function(x) sum(!is.na(x)) >= 30) %>%
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# remove intrisic R
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select(!matches(paste(intrinsic_res, collapse = "|")))
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