Batch load LDSC log file
GWASLab provides a standalone function for batch loading ldsc log file into a pd.DataFrame
.
GWASLab uses regular expression to match the values and fill them into a dataframe.
gl.read_ldsc()
Opions
filelist
:list
.A list of paths to ldsc log filesmode
:string
.h2
orrg
.
Example
Example
#mode=h2
paths = [
'/home/he/work/GWASTutorial/08_LDSC/BBJ_HDLC.log',
'/home/he/work/GWASTutorial/08_LDSC/BBJ_LDLC.log'
]
df = gl.read_ldsc(ldsc_file_list, mode="h2")
Loading file 1 :/home/he/work/GWASTutorial/08_LDSC/BBJ_HDLC.log ...
Loading file 2 :/home/he/work/GWASTutorial/08_LDSC/BBJ_LDLC.log ...
df
Filename h2_obs h2_se Lambda_gc Mean_chi2 Intercept Intercept_se Ratio Ratio_se
BBJ_HDLC.log 0.1583 0.0281 1.1523 1.2843 1.0563 0.0114 0.1981 0.0402
BBJ_LDLC.log 0.0743 0.0123 1.0833 1.1465 1.0296 0.0107 0.2019 0.0727
Example
#mode=rg
paths = [
'/home/he/work/GWASTutorial/08_LDSC/BBJ_HDLC_LDLC.log',
]
df = gl.read_ldsc(paths, mode="rg")
Loading file 1 :/home/he/work/GWASTutorial/08_LDSC/BBJ_HDLC_LDLC.log ...
df
p1 p2 rg se z p h2_obs h2_obs_se h2_int h2_int_se gcov_int gcov_int_se
BBJ_HDLC.sumstats.gz BBJ_LDLC.sumstats.gz 0.1601 0.1821 0.8794 0.3792 0.0543 0.0211 1.0583 0.0335 -0.0198 0.0121
plot ldsc rg (under construction)
For genetic correlation, after loading, you can use gl.plot_rg()
to plot a heat map to visualize the results. No extra manipulation needed.