| multiplier |
during parameter searching, the set [1..6] that was chosen |
| MSRSI_non_integerness |
median of segment residuals from segment integer copy number states |
| MBRSI_dispersion_non_integerness |
median of bin residuals from segment integer copy number states |
| MBRSM_dispersion |
median of bin residuals from segment median copy number values |
| autocorrelation_hmmcopy |
hmmcopy copy autocorrelation |
| cv_hmmcopy |
|
| empty_bins_hmmcopy |
number of empty bins in hmmcopy |
| mad_hmmcopy |
median absolute deviation of hmmcopy copy |
| mean_hmmcopy_reads_per_bin |
mean reads per hmmcopy bin |
| median_hmmcopy_reads_per_bin |
median reads per hmmcopy bin |
| std_hmmcopy_reads_per_bin |
standard deviation value of reads in hmmcopy bins |
| total_mapped_reads_hmmcopy |
total mapped reads in all hmmcopy bins |
| total_halfiness |
summed halfiness penality score of the cell |
| scaled_halfiness |
summed scaled halfiness penalty score of the cell |
| mean_state_mads |
mean value for all median absolute deviation scores for each state |
| mean_state_vars |
variance value for all median absolute deviation scores for each state |
| mad_neutral_state |
median absolute deviation score of the neutral 2 copy state |
| breakpoints |
number of breakpoints, as indicated by state changes not at the ends of chromosomes |
| mean_copy |
mean hmmcopy copy value |
| state_mode |
the most commonly occuring state |
| log_likelihood |
hmmcopy log likelihood for the cell |
| true_multiplier |
the exact decimal value used to scale the copy number for segmentation |
| cell_id |
label of the cell |
| order |
order of the cell in the hierarchical clustering tree |
| index_sequence |
index sequence of the adaptor sequence |
| column |
column of the cell on the nanowell chip |
| img_col |
column of the cell from the perspective of the microscope |
| index_i5 |
id of the i5 index adapter sequence |
| sample_type |
type of the sample |
| primer_i7 |
id of the i5 index primer sequence |
| experimental_condition |
experimental treatment of the cell, includes controls |
| index_i7 |
id of the i7 index adapter sequence |
| cell_call |
living/dead classification of the cell based on staining usually, C1 == living, C2 == dead |
| sample_id |
name of the sample |
| primer_i5 |
id of the i5 index primer sequence |
| row |
row of the cell on the nanowell chip |
| is_contaminated |
boolean, set to True if most reads belong to a different genome |