| msec_summarized {MicroSEC} | R Documentation |
An example mutation file.
Description
A dataset containing the information of eight mutations processed by the fun_homology function.
Usage
msec_summarized
Format
A list with 52 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
- mut_type
mutation type
- alt_length
length of the mutated bases
- total_read
number of mutation supporting reads
- soft_clipped_read
number of soft-clipped reads
- flag_hairpin
number of reads produced by hairpin structure
- hairpin_length
maximum length of palindromic sequences
- pre_support_length
maximum 5'-supporting length
- post_support_length
maximum 3'-supporting length
- short_support_length
minimum supporting length
- pre_minimum_length
minimum 5'-supporting length
- post_minimum_length
minimum 3'-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
- pre_rep_status
5'-repeat sequence length
- post_rep_status
3'-repeat sequence length
- homopolymer_status
homopolymer sequence length
- indel_status
whether the mutation is indel or not
- indel_length
length of indel mutation
- distant_homology
number of reads derived from homologous regions
- penalty_pre
5'-penalty score by the mapper
- penalty_post
3'-penalty score by the mapper
- caution
comment
- distant_homology_rate
rate of reads derived from homologous regions
- pre_minimum_length_adj
adjusted pre_minimum_length
- post_minimum_length_adj
adjusted pre_minimum_length
- pre_support_length_adj
adjusted pre_minimum_length
- post_support_length_adj
adjusted pre_minimum_length
- shortest_support_length_adj
the shortest short_support_length
- minimum_length_1
theoretically minimum 5'-supporting length
- minimum_length_2
theoretically minimum 3'-supporting length
- minimum_length
theoretically minimum supporting length
- short_support_length_adj
adjusted short_support_length
- altered_length
substituted/inserted length
- half_length
half of the read length
- short_support_length_total
range of short_support_length
- pre_support_length_total
range of pre_support_length
- post_support_length_total
range of post_support_length
- half_length_total
range of possible short_support_length
- total_length_total
range of possible supporting length
- soft_clipped_rate
rate of soft clipped reads
...