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hugheylab / phers

https://phers.hugheylab.org
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lintr found issues with code #29

Closed github-actions[bot] closed 2 years ago

github-actions[bot] commented 2 years ago
  1. R/genetic_association.R line 41: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/genetic_association.R#L41) 
    diseaseId = disease_id = snp = allele_count = count = N = vid = NULL
  2. R/genetic_association.R line 120: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/genetic_association.R#L120) 
    lower = melt = pval = se = upper = allele_count = varName = n_het = n_hom =
  3. R/genetic_association.R line 121: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/genetic_association.R#L121) 
    n_total = n_wt = NULL
  4. R/genetic_association.R line 135: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/genetic_association.R#L135) 
    lmInput1[, allele_count := as.factor(allele_count)]
  5. R/phers.R line 32: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/phers.R#L32) 
    flag = icd = person_id = . = NULL
  6. R/phers.R line 78: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/phers.R#L78) 
    phecode = person_id = . = prev = w = NULL
  7. R/phers.R line 111: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/phers.R#L111) 
    person_id = phecode = disease_id = w = score = . = NULL
  8. R/phers.R line 155: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/phers.R#L155) 
    disease_id = diseaseId = r_score = . = person_id = score = NULL
  9. R/phers.R line 173: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/phers.R#L173) 
    rOut[, r_score := rstandard(rFit)]})
  10. R/positive_control.R line 22: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/positive_control.R#L22) 
    dx_status = NULL
  11. R/positive_control.R line 35: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/positive_control.R#L35) 
    cases[, dx_status := 1]
  12. R/positive_control.R line 40: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/positive_control.R#L40) 
    dxStatus[is.na(dx_status), dx_status := 0]
  13. R/utils.R line 99: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/utils.R#L99) 
    n_het = n_hom = n_wt = NULL
  14. R/utils.R line 102: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/utils.R#L102) 
    dCounts[, n_wt := sum(lmInput$allele_count == 0)]
  15. R/utils.R line 103: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/utils.R#L103) 
    dCounts[, n_het := sum(lmInput$allele_count == 1)]
  16. R/utils.R line 104: Variable and function name style should be camelCase. (https://github.com/hugheylab/phers/blob/josh-code-review-examples/R/utils.R#L104) 
    dCounts[, n_hom := sum(lmInput$allele_count == 2)]