Date created
2024-09-26
Resource type
Authors/Contributors
Author: Chhina, Avneet Kaur
Abstract
This file contains information on 26 variables for 34 studies and is used as the input file for Appendix D: R code file for figures, tables, and statistical analysis. Some variables included in this file are organism examined, its classification based on taxa, number of individuals, populations, genome-wide SNPs, putatively adaptive SNPs, and proportion of putatively adaptive SNPs along with information on the type of sequencing used for genome-wide SNPs and method used to identify putatively adaptive SNPs. Information on the observed and expected Spearman correlation as well as study-wide FST and allele frequencies is provided.
Description
See section 3.6 "Details of studies included in the analysis" in the thesis for further information about each data source. A subset of variables included in "Details_of_34_Studies.csv" file are defined below:
account_for_nps_or_dh_or_false_positives - This column indicates information on whether the type of analyses used to detect putatively adaptive SNPs for each study accounted for neutral population structure (nps) or impact of population demography (dh) or contributed to reduction in false-positives. In this column, no is indicated by “0” and means no tests accounted for it, yes is indicated by “1” and means all tests accounted for it in some way, and mixed is indicated by “0.5” and means some tests did.
Weir_cockerham_software_wc_hierfstat - This column indicates study-wide FST values.
allele_frequency_2_corrected_random_to_adaptive_mann_whittney - This column indicates p-values from Mann-Whittney U-test. This test compared the median minor allele frequencies of random and putatively adaptive SNPs.
allele_frequency_2_corrected_neutral_to_adaptive_corrected_mann_whittney - This column indicates p-values from Mann-Whittney U-test. This test compared the median minor allele frequencies of neutral and putatively adaptive SNPs.
neutral_2_median - Median value of minor allele frequencies of neutral SNPs.
adaptive_2_median - Median value of minor allele frequencies of putatively adaptive SNPs.
random_2_median - Median value of minor allele frequencies of random SNPs.
var_shapley_raw_genome_wide - variance of Shapley Values of raw genome-wide SNPs.
account_for_nps_or_dh_or_false_positives - This column indicates information on whether the type of analyses used to detect putatively adaptive SNPs for each study accounted for neutral population structure (nps) or impact of population demography (dh) or contributed to reduction in false-positives. In this column, no is indicated by “0” and means no tests accounted for it, yes is indicated by “1” and means all tests accounted for it in some way, and mixed is indicated by “0.5” and means some tests did.
Weir_cockerham_software_wc_hierfstat - This column indicates study-wide FST values.
allele_frequency_2_corrected_random_to_adaptive_mann_whittney - This column indicates p-values from Mann-Whittney U-test. This test compared the median minor allele frequencies of random and putatively adaptive SNPs.
allele_frequency_2_corrected_neutral_to_adaptive_corrected_mann_whittney - This column indicates p-values from Mann-Whittney U-test. This test compared the median minor allele frequencies of neutral and putatively adaptive SNPs.
neutral_2_median - Median value of minor allele frequencies of neutral SNPs.
adaptive_2_median - Median value of minor allele frequencies of putatively adaptive SNPs.
random_2_median - Median value of minor allele frequencies of random SNPs.
var_shapley_raw_genome_wide - variance of Shapley Values of raw genome-wide SNPs.
| Download file | Size |
|---|---|
| Details_of_34_studies.csv | 10.08 KB |
Identifier
etd23351
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