Check if genes/features are present — Feature

Check if genes are present in object and return vector of found genes. Return warning messages for genes not found.

Feature_Present(
  data,
  features,
  case_check = TRUE,
  case_check_msg = TRUE,
  print_msg = TRUE,
  omit_warn = TRUE,
  return_none = FALSE,
  seurat_assay = NULL
)

Arguments

data: Name of input data. Currently only data of classes: Seurat, liger, data.frame, dgCMatrix, dgTMatrix, tibble are accepted. Gene_IDs must be present in rownames of the data.
features: vector of features to check.
case_check: logical. Whether or not to check if features are found if the case is changed from the input list (Sentence case to Upper and vice versa). Default is TRUE.
case_check_msg: logical. Whether to print message to console if alternate case features are found in addition to inclusion in returned list. Default is TRUE.
print_msg: logical. Whether message should be printed if all features are found. Default is TRUE.
omit_warn: logical. Whether to print message about features that are not found in current object. Default is TRUE.
return_none: logical. Whether list of found vs. bad features should still be returned if no features are found. Default is FALSE.
seurat_assay: Name of assay to pull feature names from if data is Seurat Object. Default is NULL which will check against features from all assays present.

Value

A list of length 3 containing 1) found features, 2) not found features, 3) features found if case was modified.

Examples

if (FALSE) {
features <- Feature_Present(data = obj_name, features = DEG_list, print_msg = TRUE,
case_check = TRUE)
found_features <- features[[1]]
}