scCustomize (version 3.0.1)

Feature_Present: Check if genes/features are present

Description

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

Usage

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

Value

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

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.

Examples

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