ad_rd100: Arabidopsis RD100 data.

In ruolin/raspberry: Differential spliced transcripts analysis based on multinomial logistic regression

Description

Exonpath counts and various information for 4961 multi-isoforms genes from 6 arabidopsis thaliana samples. These 6 samples are from two groups. A dataset contains a list of 6 lists, corresponding to one sample. Each sample contains a list of genes and each gene is a data frame. These lists and tables are generated by Strawberry https://github.com/ruolin/strawberry, which is a cpp program that efficiently analyzes each RNA-Seq alignment file (BAM) and produces these tables.

Usage

ad_rd100

Format

Gene data frame with 16 variables and each line represent a exonpath:

sample

sample name, as a string.

sample_frag_count

total fragment count for a sample.

gene_id

gene ID.

gene_frag_count

total fragment count for a gene.

transcripts

transcript ids, comma separated.

FPKMs

trainscript FPKM(Fragments Per Kilobase of transcript per Million mapped reads), comma separated.

conditional_probabilities

Conditional on a transcript, the probability of a read generated by a exonpath, comma separated.

class_probabilities

Probability of a read generated by a transcript, comma separated.

path_symbol

a unique id for a exonpath, indicating the genomic locations.

path_count

exonpath fragment count

path_gc_content

the GC content of a exonpath

path_hexmer_entropy

the averaged hexmer entropy fo a exonpath

gc_stretch_0.8_20

A indicator indicating whether the exonpath contains a stretch of DNA at least 20bp and have gc ratio > 0.8

gc_stretch_0.8_40

A indicator indicating whether the exonpath contains a stretch of DNA at least 40bp and have gc ratio > 0.8

gc_stretch_0.9_20

A indicator indicating whether the exonpath contains a stretch of DNA at least 20bp and have gc ratio > 0.9

gc_stretch_0.9_40

A indicator indicating whether the exonpath contains a stretch of DNA at least 40bp and have gc ratio > 0.9

Source

http://https://github.com/ruolin/raspberry

Examples

data("ad_rd100")

ruolin/raspberry documentation built on Jan. 1, 2020, 8:39 a.m.