Question: ExAC PLI score calculation
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3.8 years ago by
Hello all,
could you please simply explain for me how PLI score has been calculated? can we use it to filter the list of variants? How can we justify that BRCA1 has pLI = 0.00 ?
Please don't point me to ExAC paper, I read it and I am totally confused now! Thanks Sara
ADD COMMENT • link • modified 3.8 years ago • written 3.8 years ago by jonessara770 • 220
And what about the supplementary of the paper (part 4.1)?
Also, from the FAQ:
What are the constraint metrics? For synonymous and missense, we created a signed Z score for the deviation of observed counts from the expected number. Positive Z scores indicate increased constraint (intolerance to variation) and therefore that the gene had fewer variants than expected. Negative Z scores are given to genes that had a more variants than expected.
For LoF, we assume that there are three classes of genes with respect to tolerance to LoF variation: null (where LoF variation is completely tolerated), recessive (where heterozygous LoFs are tolerated), and haploinsufficient (where heterozygous LoFs are not tolerated). We used the observed and expected variants counts to determine the probability that a given gene is extremely intolerant of loss-of-function variation (falls into the third category). The closer pLI is to one, the more LoF intolerant the gene appears to be. We consider pLI >= 0.9 as an extremely LoF intolerant set of genes.
ADD REPLY • link written 3.8 years ago by WouterDeCoster ♦ 44k
I am wondering why the authors don't provide a formula?
ADD REPLY • link written 4 months ago by Shicheng Guo • 8.5k
Aa_somani
Manoj-gaikwad-patil
Ritesh-nandanwar
Prakash-sharma1
Priyanka-pp
Basheer-m-shafout
Vaishali Chouhan
Bnp.sewal
Thatchayani91189
monica_talwar80
Hi,I am working in a construction company. Can anybody send me the format of salary structure with PLI.
Can anybody send me the salary breakup of Rs 950000 LPA which includes PLI, LTA, HRA etc.
Please help
Regards
Monica
9711899220
From India, Chandigarh
Gurgaon HR
Dear Monica,Find below the sample for your reference :-
Basic 40,000.00
HRA 20,000.00
Conveyance Allowance 800.00
Special Allowance 5450.00
Education Allowance 200.00
Gross Monthly 66,450.00
Gross Annual (A) 797400
Provident Fund Employer 57,600.00
Statutory Bonus 40,000.00
Medical 15,000.00
LTA 40,000.00
Annual Benefits (B) 152,600.00
Total Cost To Company (A+B) (Per Annum) 950,000.00
Chill HR !!
From India, Gurgaon
Gurgaon HR
Monica Find the attached excel sheet if you are very particular in percentage bifurcation. Acknowledge it. Chill HR From India, Gurgaon
CTC Calculation Excel.xls (10.0 KB, 21396 views) |
aa_somani
Hello Monica Format in excel is attached herewith this will help you to calculate TDS and PF.. and monthly salary structure... From India, Pune
Computation A.Y. 13-14.xls (38.5 KB, 7940 views) |
bnp.sewal
Dear All seniors greeting of the day Pls. provide me 260000 CTC calculation .including Bonus, gratuity EPF,& if any others From India, Chandigarh
Dear All, Please let me know How to calculate 1. Basic 2. HRA 3. SPA 4. Conveyance ???????????? I know only Take Home salary..... Please reply ASAP... Thanks & Regards Abhishek KN
From India, Raipur
Pli Calculator Excel Download Software
Vaishali Chouhan
Pli Calculator 2019 Excel Download
Dear All, Please let me know How to calculate if salary 15000 Per Month 1. Basic 2. HRA 3. Conveyance 4. PF (Both employer & employee side) Equal Inhand salary, Please reply ASAP.From India, Indore
thatchayani91189
Dear All, Please let me know How to calculate 1. Basic 2. HRA 3. SPA 4. Conveyance ???????????? I know only Take Home salary..... Please reply ASAP... From India, Chennai
Anonymous
Hi,I am working in a HOTEL. Can anybody send me the format of salary structure with Basic,DA,HRA,CON.MEDICAL & OTHERS
Can anybody send me the salary breakup of Rs 40000/-monthly without pf deduction.(If basic+da =above 15000/- than pf is not applicable maybe)
Please help
Regards
Pramod Singh (Bangalore)
9243039418
From India, Bangalore
manoj-gaikwad-patil
Dear All, I need step by step procedure of pf chalan from salary to transaction details. From India
1
Pli Calculator Excel Download Template
#Listed In:take home salaryCity-India-Chandigarhsalary ssalary structurectc calculationsalary breakupconstruction companypf deductioncost to companyCountry-India