Function reference • ScreenR

Object

Function for the ScreenR Object

create_edger_obj(): Create edgeR Object

create_screenr_object(): Create the ScreenR Object

get_annotation_table(): Get ScreenR annotation table

get_count_table(): Get ScreenR count table

get_data_table(): Get ScreenR data_table

get_groups(): Get ScreenR groups

get_normalized_count_table(): Get ScreenR normalized_count_table

get_replicates(): Get ScreenR replicates

set_annotation_table(): Set ScreenR annotation table

set_count_table(): Set ScreenR count table

set_data_table(): Set ScreenR data_table

set_groups(): Set ScreenR groups

set_normalized_count_table(): Set ScreenR normalized_count_table

set_replicates(): Set ScreenR replicates

Computation

Function used to perform computations

barcode_lost(): Count number of barcode lost

compute_data_table(): Compute data Table

compute_metrics(): Compute Metrics

compute_slope(): Compute Slope of a Gene

count_mapped_reads(): Count the number of mapped read

mapped_reads(): Mapped Reads

normalize_data(): Normalize data

remove_all_zero_row(): Remove rows that have zero count in all samples

Find Hit

Function used to find hits

find_camera_hit(): Find Camera Hit

find_common_hit(): Find common hit

find_roast_hit(): Find Roast Hit

find_robust_zscore_hit(): Title Find robust Z-score Hit

find_zscore_hit(): Title Find Z-score Hit

Further Optimization

Function to further optimize the hit found

filter_by_slope(): Filter using the slope filter

filter_by_variance(): Filter using the variance filter

Plot

Functions used to visualize the data

plot_barcode_hit(): Plot barcode hit

plot_barcode_lost(): Plot number of barcode lost

plot_barcode_lost_for_gene(): Plot number of barcode lost for gene

plot_barcode_trend(): Plot the trend over time of the barcodes

plot_boxplot(): Plot Barcodes Hit

plot_common_hit(): Plot common hit

plot_explained_variance(): Plot the explained variance by the PC

plot_mapped_reads(): Plot mapped reads

plot_mapped_reads_distribution(): Plot the distribution of the mapped reads

plot_mds(): Multidimensional Scaling Plot

plot_trend(): Plot the trend hit gene

plot_zscore_distribution(): Plot distribution Z-score

Data

Example of data used in the ScreenR pipeline

annotation_table: Table for the annotation of Barcode

count_table: Table of the count table