| msec_analyzed {MicroSEC} | R Documentation |
An example mutation file.
Description
A dataset containing the information of eight mutations processed by the fun_homology function.
Usage
msec_analyzed
Format
A list with 37 factors, each contains 29 variables
- Sample
sample name
- Mut_type
mutation type
- Chr
altered chromosome
- Pos
altered position
- Ref
reference base
- Alt
altered base
- SimpleRepeat_TRF
mutation locating repeat sequence
- Neighborhood_sequence
neighborhood sequence
- read_length
read length
- total_read
number of mutation supporting reads
- soft_clipped_read
number of soft-clipped reads
- flag_hairpin
number of reads produced by hairpin structure
- pre_support_length
maximum 5'-supporting length
- post_support_length
maximum 3'-supporting length
- short_support_length
minimum supporting length
- pre_farthest
5'-farthest supported base from the mutated base
- post_farthest
3'-farthest supported base from the mutated base
- low_quality_base_rate_under_q18
low quality base rate
- low_quality_pre
low quality base rate of 5'- side
- low_quality_post
low quality base rate of 3'- side
- distant_homology_rate
rate of reads derived from homologous regions
- soft_clipped_rate
rate of soft clipped reads
- prob_filter_1
possibility of short-supporting length
- prob_filter_3_pre
possibility of 5'-supporting length
- prob_filter_3_post
possibility of 3'-supporting length
- filter_1_mutation_intra_hairpin_loop
filter 1
- filter_2_hairpin_structure
filter 2
- filter_3_microhomology_induced_mutation
filter 3
- filter_4_highly_homologous_region
filter 4
- filter_5_soft_clipping
filter 5
- filter_6_simple_repeat
filter 6
- filter_7_mutation_at_homopolymer
filter 7
- filter_8_low_quality
filter 8
- msec_filter_123
any of filter 1-3
- msec_filter_1234
any of filter 1-4
- msec_filter_all
any of filter 1-8
- comment
comment
...