Scoring and Marker Selection Method Based on Modified TF-IDF

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Documentation for package ‘smartid’ version 1.5.0

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cal_score calculate combined score
cal_score-method calculate combined score
cal_score_init Calculate score for each feature in each cell
gs_score compute overall score based on the given marker list
gs_score-method compute overall score based on the given marker list
gs_score_init Calculate scores of each cell on given features
iae standard inverse average expression
iae_hdb inverse average expression using hdbscan cluster as label
iae_igm labeled inverse average expression: IGM
iae_m inverse average expression: max
iae_prob labeled inverse average expression: probability based
iae_rf labeled inverse average expression: relative frequency
iae_sd inverse average expression using standard deviation (SD)
idf standard inverse cell frequency
idf_hdb inverse document frequency using hdbscan cluster as label
idf_iae_methods Get names of available IDF and IAE methods
idf_igm labeled inverse cell frequency: IGM
idf_m inverse cell frequency: max
idf_prob labeled inverse cell frequency: probability based
idf_rf labeled inverse cell frequency: relative frequency
idf_sd inverse cell frequency using standard deviation (SD)
markers_hdbscan select markers using HDBSCAN method
markers_mclust select markers using mclust EM method
markers_mixmdl select markers using mixtools EM method
ova_score_boxplot boxplot of features overall score
scale_mgm scale by mean of group mean for imbalanced data
score_barplot barplot of processed score
sim_sce_test scRNA-seq test data of 4 groups simulated by 'splatter'.
sin_score_boxplot boxplot of split single feature score
tf compute term/feature frequency within each cell
top_markers scale score and return top markers
top_markers-method scale score and return top markers
top_markers_abs calculate group median, MAD or mean score and order genes based on scores
top_markers_glm calculate group mean score using glm and order genes based on scores difference
top_markers_init compute group summarized score and order genes based on processed scores